Package: gmapR

Version: 1.22.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:gmapR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings gmapR_1.22.0.tar.gz

StartedAt: 2018-10-16 00:53:10 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:58:41 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 331.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gmapR.Rcheck

Warnings: 5

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:gmapR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings gmapR_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/gmapR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gmapR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gmapR’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following files with non-portable file names:
  src/gmap/config/lt˜obsolete.m4
  src/gstruct/config/lt˜obsolete.m4
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gmapR’ can be installed ... WARNING
Found the following significant warnings:
  WARNING: You don't seem to have gsnap specified.
  gmap.c:3244:28: warning: passing argument 11 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types]
  gmap.c:3244:37: warning: passing argument 12 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types]
  table.c:283:18: warning: passing argument 1 of ‘keyfree’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:302:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:368:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:434:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:526:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:653:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2170:11: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2442:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2442:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2456:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2499:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2499:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2513:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2643:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2643:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2656:36: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2699:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2699:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2712:12: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:2752:11: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3024:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3024:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3038:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3082:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3082:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3096:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3217:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3217:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3231:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3274:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3274:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  sarray-read.c:3288:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/biocbuild/bbs-3.7-bioc/meat/gmapR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 77.7Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    extdata   5.6Mb
    libs      1.9Mb
    usr      68.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘AnnotationDbi’
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘S4Vectors:::labeledLine’
  ‘S4Vectors:::new_SimpleList_from_list’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkTallyConsistency: no visible binding for global variable
  ‘count.plus’
checkTallyConsistency: no visible binding for global variable
  ‘count.minus’
checkTallyConsistency: no visible binding for global variable
  ‘count.plus.ref’
checkTallyConsistency: no visible binding for global variable
  ‘count.minus.ref’
fieldNames: no visible global function definition for
  ‘R_iit_fieldNames’
newGmapAlignerParam: ... may be used in an incorrect context:
  ‘list(...)’
open.IITFile: no visible binding for global variable ‘R_iit_read’
open.IITFile: no visible global function definition for ‘resource’
typeNames: no visible global function definition for ‘R_iit_typeNames’
variantSummary: no visible binding for global variable ‘count.total’
variantSummary: no visible binding for global variable ‘count.ref’
variantSummary: no visible binding for global variable ‘count’
import,IITFile-ANY-ANY: no visible global function definition for
  ‘checkArgFormat’
import,IITFile-ANY-ANY: no visible binding for global variable
  ‘R_iit_read’
snps<-,GmapSnpDirectory-character-VCF: no visible global function
  definition for ‘rowData’
Undefined global functions or variables:
  R_iit_fieldNames R_iit_read R_iit_typeNames checkArgFormat count
  count.minus count.minus.ref count.plus count.plus.ref count.ref
  count.total resource rowData
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘GmapParam’ ‘gmap’
Undocumented S4 classes:
  ‘GmapAlignerParam’ ‘GmapParam’
Undocumented S4 methods:
  generic 'as.character' and siglist 'GmapGenomeDirectory'
  generic 'bamPaths' and siglist 'GmapAlignerOutput'
  generic 'gmap' and siglist 'ANY,GmapParam'
  generic 'gmap' and siglist 'FastaFile,GmapParam'
  generic 'gmap' and siglist 'character,GmapParam'
  generic 'path' and siglist 'GmapAlignerOutput'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/gmapR/libs/gmapR.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘gmapR_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/gmapR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL gmapR
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘gmapR’ ...
** libs
** arch - 
rm -rf samtools; mkdir samtools
ln -sf /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libbam.a samtools/libbam.a
for header in /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include/samtools/*.h; do \
  ln -sf $header samtools/; \
done
cd gstruct/; \
        CFLAGS="-g -O3" \
./configure --enable-static --disable-shared \
            --prefix=/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr --includedir=/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include/gstruct \
            --libdir=/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib \
            --with-samtools-lib=/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/samtools \
	    --disable-maintainer-mode \
                    --disable-binaries
checking package version... 2016-06-01
checking whether to enable maintainer-specific portions of Makefiles... no
loading default site script ./config.site
checking CFLAGS... -g -O3
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin
checking whether to link statically... not specified so disabled by default
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for qsub... no
checking gmap program directory... 
checking for get-genome... false
checking for iit_store... false
checking for iit_get... false
checking for gmap_build... false
checking for gmap... false
checking for gsnap... false
checking for sam_sort... false
checking for uniqscan... false
checking for rint in -lm... yes
checking for pthreads feature... not specified so enabled by default
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for size_t... yes
checking for off_t... yes
checking for caddr_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for working mmap with MAP_FIXED... yes
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
checking for MAP_VARIABLE in mmap... no
checking for MAP_SHARED in mmap... yes
checking for MAP_PRIVATE in mmap... yes
checking for MAP_FAILED in mmap... yes
checking for MADV_DONTNEED in madvise... yes
checking for MADV_WILLNEED in madvise... yes
checking for MADV_RANDOM in madvise... yes
checking for MADV_SEQUENTIAL in madvise... yes
checking for ceil... yes
checking for floor... yes
checking for index... yes
checking for log... yes
checking for madvise... yes
checking for memcpy... yes
checking for memmove... yes
checking for memset... yes
checking for munmap... yes
checking for pow... yes
checking for rint... yes
checking for stat64... yes
checking for strtoul... yes
checking for sysconf... yes
checking for sysctl... yes
checking for sigaction... yes
checking for struct stat64... no
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... no
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for builtin popcount/clz/ctz features... not specified so enabled by default
./configure: line 16917: ACX_BUILTIN_POPCOUNT: command not found
checking for bsr instruction in assembly... yes
checking whether sse2 is enabled... not specified so enabled by default
checking compiler is defective and requires an immediate in sse2 shift commands... no
checking whether ssse3 is enabled... not specified so enabled by default
checking whether sse4.1 is enabled... not specified so enabled by default
checking whether sse4.2 is enabled... not specified so enabled by default
checking whether avx is enabled... not specified so enabled by default
checking whether avx2 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking for x86 cpuid 0x00000001 output... 406f1:15200800:7ffefbff:bfebfbff
checking whether mmx is enabled and supported by CPU... yes
checking whether sse is enabled and supported by CPU... yes
checking whether sse2 is enabled and supported by CPU... yes
checking whether sse3 is enabled and supported by CPU... yes
checking whether ssse3 is enabled and supported by CPU... yes
checking whether sse4.1 is enabled and supported by CPU... yes
checking whether sse4.2 is enabled and supported by CPU... yes
checking whether avx is enabled and supported by CPU... yes
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether avx is supported by operating system... yes
checking whether popcnt is enabled and supported by CPU... yes
checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800
checking whether lzcnt is enabled and supported by CPU... yes
checking for x86 cpuid 0x00000007 output... 0:21cbfbb:0:9c000000
checking whether avx2 is enabled and supported by CPU... yes
checking whether bmi1 is enabled and supported by CPU... yes
checking whether bmi2 is enabled and supported by CPU... yes
checking whether C compiler accepts -mmmx... yes
checking for mmintrin.h header file... yes
checking whether C compiler accepts -msse... yes
checking for xmmintrin.h header file... yes
checking whether C compiler accepts -msse2... yes
checking for emmintrin.h header file... yes
checking whether C compiler accepts -msse3... yes
checking for pmmintrin.h header file... yes
checking whether C compiler accepts -mssse3... yes
checking for tmmintrin.h header file... yes
checking whether C compiler accepts -msse4.1... yes
checking for smmintrin.h header file... yes
checking whether C compiler accepts -msse4.2... yes
checking for nmmintrin.h header file... yes
checking whether C compiler accepts -mavx... yes
checking for immintrin.h header file... yes
checking whether C compiler accepts -mavx2... yes
checking for immintrin.h header file... yes
checking gmapdb... /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share
checking whether to make binaries... disabled
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for samtools program... checking for samtools library... provided by --with-samtools-lib
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating lib/gstruct-1.0.pc
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING:

WARNING: You don't seem to have gsnap specified.

checking Standard compiler and flags to be used... gcc -g -O3
checking Standard linker flags to be used... 
checking pthread compiler flags to be used... -pthread
checking popcnt compiler flags to be used... 
checking SIMD features available on computer...  mmx sse sse2 sse3 ssse3 sse4.1 sse4.2 avx avx2
checking SIMD compiler flags to be used...  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2
cd gstruct; \
make install
make[1]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct'
Making install in src
make[2]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct/src'
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o libgstruct_1.0_la-except.lo `test -f 'except.c' || echo './'`except.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c except.c -o libgstruct_1.0_la-except.o
mv -f .deps/libgstruct_1.0_la-except.Tpo .deps/libgstruct_1.0_la-except.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c -o libgstruct_1.0_la-assert.lo `test -f 'assert.c' || echo './'`assert.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o
mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o
mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o
mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o
mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:296:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:457:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:758:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o libgstruct_1.0_la-interval.o
mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o
mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o
mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o
access.c: In function ‘Access_file_exists_p’:
access.c:59:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:39:0:
access.c: In function ‘Access_allocated’:
littleendian.h:18:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(unsigned int),n,fp)
                             ^
access.c:125:3: note: in expansion of macro ‘FREAD_UINTS’
   FREAD_UINTS(memory,(*len)/eltsize,fp);
   ^
mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2345:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2611:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1723:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1724:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1725:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1726:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1727:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1808:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1809:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1811:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1815:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:20:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1899:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:16:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp)
                          ^
iit-read.c:1905:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2249:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2255:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2260:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(unsigned int));
     ^
iit-read.c:2271:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2277:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2282:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(unsigned int));
     ^
iit-read.c:2293:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:15:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:3011:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:20:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:2022:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:16:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(unsigned int),1,fp)
                          ^
iit-read.c:2027:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o
mv -f .deps/libgstruct_1.0_la-chrom.Tpo .deps/libgstruct_1.0_la-chrom.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o
mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o
mv -f .deps/libgstruct_1.0_la-md5.Tpo .deps/libgstruct_1.0_la-md5.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o
mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o
genome.c: In function ‘fill_buffer’:
genome.c:1218:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:329:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:1374:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:1451:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:1554:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:1710:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o
mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o
mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c chrnum.c -o libgstruct_1.0_la-chrnum.o
mv -f .deps/libgstruct_1.0_la-chrnum.Tpo .deps/libgstruct_1.0_la-chrnum.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c -o libgstruct_1.0_la-bamread.lo `test -f 'bamread.c' || echo './'`bamread.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c bamread.c -o libgstruct_1.0_la-bamread.o
mv -f .deps/libgstruct_1.0_la-bamread.Tpo .deps/libgstruct_1.0_la-bamread.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c -o libgstruct_1.0_la-samread.lo `test -f 'samread.c' || echo './'`samread.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c samread.c -o libgstruct_1.0_la-samread.o
mv -f .deps/libgstruct_1.0_la-samread.Tpo .deps/libgstruct_1.0_la-samread.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c -o libgstruct_1.0_la-parserange.lo `test -f 'parserange.c' || echo './'`parserange.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c parserange.c -o libgstruct_1.0_la-parserange.o
mv -f .deps/libgstruct_1.0_la-parserange.Tpo .deps/libgstruct_1.0_la-parserange.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c -o libgstruct_1.0_la-tableuint.lo `test -f 'tableuint.c' || echo './'`tableuint.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c tableuint.c -o libgstruct_1.0_la-tableuint.o
mv -f .deps/libgstruct_1.0_la-tableuint.Tpo .deps/libgstruct_1.0_la-tableuint.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c -o libgstruct_1.0_la-iit-write.lo `test -f 'iit-write.c' || echo './'`iit-write.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c iit-write.c -o libgstruct_1.0_la-iit-write.o
mv -f .deps/libgstruct_1.0_la-iit-write.Tpo .deps/libgstruct_1.0_la-iit-write.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c -o libgstruct_1.0_la-ucharlist.lo `test -f 'ucharlist.c' || echo './'`ucharlist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c ucharlist.c -o libgstruct_1.0_la-ucharlist.o
mv -f .deps/libgstruct_1.0_la-ucharlist.Tpo .deps/libgstruct_1.0_la-ucharlist.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c -o libgstruct_1.0_la-matchpool.lo `test -f 'matchpool.c' || echo './'`matchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c matchpool.c -o libgstruct_1.0_la-matchpool.o
mv -f .deps/libgstruct_1.0_la-matchpool.Tpo .deps/libgstruct_1.0_la-matchpool.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o
mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo `test -f 'tally.c' || echo './'`tally.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o
mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o
mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o
bamtally.c: In function ‘print_allele_counts_simple’:
bamtally.c:1262:18: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=]
       fprintf(fp,"%s %ld ref:%ld",
                  ^
bamtally.c:1274:18: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=]
       fprintf(fp,"%s %ld ref:%ld",
                  ^
bamtally.c:1286:18: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int’ [-Wformat=]
       fprintf(fp,"%s %ld ref:%ld",
                  ^
bamtally.c:1305:16: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int’ [-Wformat=]
     fprintf(fp," _%ld",this->delcounts_plus + this->delcounts_minus);
                ^
bamtally.c: In function ‘print_zeroes’:
bamtally.c:1561:9: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
  printf(">%ld %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);
         ^
bamtally.c:1576:9: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
  printf(">%ld %s:%u..%u\n",/*total*/0,printchr,blockstart,blockend-1U);
         ^
bamtally.c: In function ‘print_block’:
bamtally.c:3639:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
      printf(" ref:%ld",insertion_refcount(&refcount_plus,ins0,alloc_tallies,alloc_low,alloc_high,max_softclip));
             ^
bamtally.c:3642:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);
             ^
bamtally.c:3642:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int’ [-Wformat=]
bamtally.c:3844:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
      printf(" ref:%ld",deletion_refcount(&refcount_plus,del0,alloc_tallies,alloc_low,alloc_high,max_softclip));
             ^
bamtally.c:3847:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);
             ^
bamtally.c:3847:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int’ [-Wformat=]
bamtally.c:4050:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
      printf(" ref:%ld",minv_refcount(&refcount_plus,minv0,alloc_tallies,alloc_low,alloc_high,max_softclip));
             ^
bamtally.c:4053:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
      printf(" ref:%ld|%ld",refcount_plus,refcount - refcount_plus);
             ^
bamtally.c:4053:13: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int’ [-Wformat=]
bamtally.c:4197:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
       printf("(%ld@%d",this->matches_byshift_minus[shift],-shift);
              ^
bamtally.c:4200:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
       printf(",%ld@%d",this->matches_byshift_minus[shift],-shift);
              ^
bamtally.c:4208:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
       printf("(%ld@%d",this->matches_byshift_plus[shift],shift);
              ^
bamtally.c:4211:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
       printf(",%ld@%d",this->matches_byshift_plus[shift],shift);
              ^
bamtally.c:4240:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
       printf("(%ldNM%d",this->matches_bynm[nm],nm);
              ^
bamtally.c:4243:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
       printf(",%ldNM%d",this->matches_bynm[nm],nm);
              ^
bamtally.c:4285:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
       printf("(%ldXS",this->matches_byxs[xs]);
              ^
bamtally.c:4288:14: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘int’ [-Wformat=]
       printf(",%ldXS",this->matches_byxs[xs]);
              ^
mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c -o libgstruct_1.0_la-datadir.lo `test -f 'datadir.c' || echo './'`datadir.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2 -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c datadir.c -o libgstruct_1.0_la-datadir.o
mv -f .deps/libgstruct_1.0_la-datadir.Tpo .deps/libgstruct_1.0_la-datadir.Plo
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -mbmi -mbmi2 -mavx2  -I. -fPIC -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3   -pthread -version-info 1:0:0  -o libgstruct-1.0.la -rpath /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib libgstruct_1.0_la-except.lo libgstruct_1.0_la-assert.lo libgstruct_1.0_la-mem.lo libgstruct_1.0_la-intlist.lo libgstruct_1.0_la-list.lo libgstruct_1.0_la-littleendian.lo libgstruct_1.0_la-bigendian.lo libgstruct_1.0_la-interval.lo libgstruct_1.0_la-uintlist.lo libgstruct_1.0_la-stopwatch.lo libgstruct_1.0_la-access.lo libgstruct_1.0_la-iit-read.lo libgstruct_1.0_la-chrom.lo libgstruct_1.0_la-genomicpos.lo libgstruct_1.0_la-md5.lo libgstruct_1.0_la-sequence.lo libgstruct_1.0_la-genome.lo libgstruct_1.0_la-uinttable.lo libgstruct_1.0_la-table.lo libgstruct_1.0_la-chrnum.lo libgstruct_1.0_la-bamread.lo libgstruct_1.0_la-samread.lo libgstruct_1.0_la-parserange.lo libgstruct_1.0_la-tableuint.lo libgstruct_1.0_la-iit-write.lo libgstruct_1.0_la-ucharlist.lo libgstruct_1.0_la-matchpool.lo libgstruct_1.0_la-mismatchpool.lo libgstruct_1.0_la-tally.lo libgstruct_1.0_la-translation.lo libgstruct_1.0_la-bamtally.lo libgstruct_1.0_la-datadir.lo  -lz -lm 
libtool: link: ar cru .libs/libgstruct-1.0.a  libgstruct_1.0_la-except.o libgstruct_1.0_la-assert.o libgstruct_1.0_la-mem.o libgstruct_1.0_la-intlist.o libgstruct_1.0_la-list.o libgstruct_1.0_la-littleendian.o libgstruct_1.0_la-bigendian.o libgstruct_1.0_la-interval.o libgstruct_1.0_la-uintlist.o libgstruct_1.0_la-stopwatch.o libgstruct_1.0_la-access.o libgstruct_1.0_la-iit-read.o libgstruct_1.0_la-chrom.o libgstruct_1.0_la-genomicpos.o libgstruct_1.0_la-md5.o libgstruct_1.0_la-sequence.o libgstruct_1.0_la-genome.o libgstruct_1.0_la-uinttable.o libgstruct_1.0_la-table.o libgstruct_1.0_la-chrnum.o libgstruct_1.0_la-bamread.o libgstruct_1.0_la-samread.o libgstruct_1.0_la-parserange.o libgstruct_1.0_la-tableuint.o libgstruct_1.0_la-iit-write.o libgstruct_1.0_la-ucharlist.o libgstruct_1.0_la-matchpool.o libgstruct_1.0_la-mismatchpool.o libgstruct_1.0_la-tally.o libgstruct_1.0_la-translation.o libgstruct_1.0_la-bamtally.o libgstruct_1.0_la-datadir.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libgstruct-1.0.a
libtool: link: ( cd ".libs" && rm -f "libgstruct-1.0.la" && ln -s "../libgstruct-1.0.la" "libgstruct-1.0.la" )
make[3]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct/src'
 /bin/mkdir -p '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libgstruct-1.0.la '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib'
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.la
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: chmod 644 /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: ranlib /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: finish: PATH="/usr/bin:/bin:/usr/local/bin:/snap/bin:/usr/local/root/bin:/usr/local/ensembl-vep-release-94:/sbin" ldconfig -n /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include/gstruct'
 /usr/bin/install -c -m 644 config.h fopen.h bool.h types.h except.h assert.h mem.h intlistdef.h intlist.h listdef.h list.h littleendian.h bigendian.h interval.h uintlist.h stopwatch.h access.h iitdef.h iit-read.h chrom.h genomicpos.h md5.h complement.h sequence.h genome.h uinttable.h table.h chrnum.h bamread.h samread.h parserange.h dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h tableuint.h iit-write.h ucharlist.h matchdef.h '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include/gstruct'
 /usr/bin/install -c -m 644 matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include/gstruct'
 /bin/mkdir -p '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig'
 /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig'
make[3]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct/src'
make[2]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct/src'
make[2]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct'
make[3]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct'
make[2]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct'
make[1]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gstruct'
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include  -g -O3 -fpic  -g -O2  -Wall -c bamreader.c -o bamreader.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include  -g -O3 -fpic  -g -O2  -Wall -c bamtally.c -o bamtally.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include  -g -O3 -fpic  -g -O2  -Wall -c iit.c -o iit.o
iit.c: In function ‘R_iit_read’:
iit.c:267:18: warning: ‘fields’ may be used uninitialized in this function [-Wmaybe-uninitialized]
           mkChar(IIT_fieldvalue(iit, i, fields[f])));
                  ^
iit.c:214:10: note: ‘fields’ was declared here
     int *fields;
          ^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include  -g -O3 -fpic  -g -O2  -Wall -c variantsummary.c -o variantsummary.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include  -g -O3 -fpic  -g -O2  -Wall -c genome.c -o genome.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/include  -I/usr/local/include  -g -O3 -fpic  -g -O2  -Wall -c R_init_gmapR.c -o R_init_gmapR.o
gcc -shared -L"/home/biocbuild/bbs-3.7-bioc/R/lib" -L/usr/local/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz  -L"/home/biocbuild/bbs-3.7-bioc/R/lib" -lR
cd gmap/; \
 ./configure --with-gmapdb= --prefix=/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr \
            --libdir=/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/lib --disable-maintainer-mode
checking package version... 2013-11-01
checking whether to enable maintainer-specific portions of Makefiles... no
checking CONFIG_SITE... ./config.site
loading script ./config.site
checking CFLAGS... not set by user so using default -O3
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of gcc... gcc3
checking bindir... /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin
checking for a working version of perl... /usr/bin/perl
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for rint in -lm... yes
checking for pthreads feature... not specified so enabled by default
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for size_t... yes
checking for off_t... yes
checking for caddr_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether mmap is enabled... not specified so enabled by default
checking for working mmap with MAP_FIXED... yes
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
checking for MAP_VARIABLE in mmap... no
checking for MAP_SHARED in mmap... yes
checking for MAP_PRIVATE in mmap... yes
checking for MAP_FAILED in mmap... yes
checking for MADV_DONTNEED in madvise... yes
checking for MADV_WILLNEED in madvise... yes
checking for MADV_RANDOM in madvise... yes
checking for MADV_SEQUENTIAL in madvise... yes
checking for ceil... yes
checking for floor... yes
checking for index... yes
checking for log... yes
checking for madvise... yes
checking for memcpy... yes
checking for memmove... yes
checking for memset... yes
checking for munmap... yes
checking for pow... yes
checking for rint... yes
checking for stat64... yes
checking for strtoul... yes
checking for sysconf... yes
checking for sysctl... yes
checking for sigaction... yes
checking for struct stat64... no
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... no
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for popcnt feature... not specified so enabled by default
checking for __builtin_popcount... yes
checking for __builtin_clz... yes
checking for __builtin_ctz... yes
checking for bsr instruction in assembly... yes
checking whether sse2 is enabled... not specified so enabled by default
checking whether user has declared a defective SSE2 compiler... no
checking whether sse4.1 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking for x86 cpuid 0x00000001 output... 406f1:1200800:7ffefbff:bfebfbff
checking whether mmx is enabled and supported... yes
checking whether sse is enabled and supported... yes
checking whether sse2 is enabled and supported... yes
checking whether sse3 is enabled and supported... yes
checking whether ssse3 is enabled and supported... yes
checking whether sse4.1 is enabled and supported... yes
checking whether sse4.2 is enabled and supported... yes
checking whether avx is enabled and supported... yes
checking whether C compiler accepts -mmmx... yes
checking whether C compiler accepts -msse... yes
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -msse3... yes
checking whether C compiler accepts -mssse3... yes
checking whether C compiler accepts -msse4.1... yes
checking whether C compiler accepts -msse4.2... yes
checking whether C compiler accepts -mavx... yes
checking gmapdb... /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share
checking MAX_READLENGTH... 250
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for bzlib support... enabled
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for BZ2_bzReadOpen in -lbz2... yes
checking for BZ2_bzRead in -lbz2... yes
checking for BZ2_bzReadClose in -lbz2... yes
checking if bzlib package is complete... working
checking for goby library... disabled
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating util/Makefile
config.status: creating util/gmap_compress.pl
config.status: creating util/gmap_uncompress.pl
config.status: creating util/gmap_process.pl
config.status: creating util/gmap_setup.pl
config.status: creating util/gmap_build.pl
config.status: creating util/gmap_reassemble.pl
config.status: creating util/md_coords.pl
config.status: creating util/fa_coords.pl
config.status: creating util/psl_splicesites.pl
config.status: creating util/psl_introns.pl
config.status: creating util/psl_genes.pl
config.status: creating util/gtf_splicesites.pl
config.status: creating util/gtf_introns.pl
config.status: creating util/gtf_genes.pl
config.status: creating util/gff3_splicesites.pl
config.status: creating util/gff3_introns.pl
config.status: creating util/gff3_genes.pl
config.status: creating util/dbsnp_iit.pl
config.status: creating util/gvf_iit.pl
config.status: creating util/vcf_iit.pl
config.status: creating tests/Makefile
config.status: creating tests/align.test
config.status: creating tests/coords1.test
config.status: creating tests/setup1.test
config.status: creating tests/iit.test
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
cd gmap; \
make install
make[1]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap'
Making install in src
make[2]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/src'
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-except.o -MD -MP -MF .deps/gmap-except.Tpo -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmap-except.Tpo .deps/gmap-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-assert.o -MD -MP -MF .deps/gmap-assert.Tpo -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmap-assert.Tpo .deps/gmap-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-mem.o -MD -MP -MF .deps/gmap-mem.Tpo -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmap-mem.Tpo .deps/gmap-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intlist.o -MD -MP -MF .deps/gmap-intlist.Tpo -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmap-intlist.Tpo .deps/gmap-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-list.o -MD -MP -MF .deps/gmap-list.Tpo -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmap-list.Tpo .deps/gmap-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-littleendian.o -MD -MP -MF .deps/gmap-littleendian.Tpo -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bigendian.o -MD -MP -MF .deps/gmap-bigendian.Tpo -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-univinterval.o -MD -MP -MF .deps/gmap-univinterval.Tpo -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
mv -f .deps/gmap-univinterval.Tpo .deps/gmap-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-interval.o -MD -MP -MF .deps/gmap-interval.Tpo -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmap-interval.Tpo .deps/gmap-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uintlist.o -MD -MP -MF .deps/gmap-uintlist.Tpo -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmap-uintlist.Tpo .deps/gmap-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stopwatch.o -MD -MP -MF .deps/gmap-stopwatch.Tpo -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmap-stopwatch.Tpo .deps/gmap-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-access.o -MD -MP -MF .deps/gmap-access.Tpo -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read-univ.o -MD -MP -MF .deps/gmap-iit-read-univ.Tpo -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/gmap-iit-read-univ.Tpo .deps/gmap-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read.o -MD -MP -MF .deps/gmap-iit-read.Tpo -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-md5.o -MD -MP -MF .deps/gmap-md5.Tpo -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gmap-md5.Tpo .deps/gmap-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bzip2.o -MD -MP -MF .deps/gmap-bzip2.Tpo -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gmap-bzip2.Tpo .deps/gmap-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-sequence.o -MD -MP -MF .deps/gmap-sequence.Tpo -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gmap-sequence.Tpo .deps/gmap-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-reader.o -MD -MP -MF .deps/gmap-reader.Tpo -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gmap-reader.Tpo .deps/gmap-reader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genomicpos.o -MD -MP -MF .deps/gmap-genomicpos.Tpo -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmap-genomicpos.Tpo .deps/gmap-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress.o -MD -MP -MF .deps/gmap-compress.Tpo -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmap-compress.Tpo .deps/gmap-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress-write.o -MD -MP -MF .deps/gmap-compress-write.Tpo -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c: In function ‘fill_buffer’:
compress-write.c:73:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
         ^
compress-write.c: In function ‘write_compressed_one’:
compress-write.c:251:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
compress-write.c: In function ‘put_compressed_one’:
compress-write.c:299:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
mv -f .deps/gmap-compress-write.Tpo .deps/gmap-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gbuffer.o -MD -MP -MF .deps/gmap-gbuffer.Tpo -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gmap-gbuffer.Tpo .deps/gmap-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome.o -MD -MP -MF .deps/gmap-genome.Tpo -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_hr.o -MD -MP -MF .deps/gmap-genome_hr.Tpo -c -o gmap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gmap-genome_hr.Tpo .deps/gmap-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_sites.o -MD -MP -MF .deps/gmap-genome_sites.Tpo -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
mv -f .deps/gmap-genome_sites.Tpo .deps/gmap-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome-write.o -MD -MP -MF .deps/gmap-genome-write.Tpo -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
genome-write.c: In function ‘genome_write_file’:
genome-write.c:252:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:252:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c:255:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:255:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c: In function ‘genome_writeraw_file’:
genome-write.c:429:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:429:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c:432:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:432:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c: In function ‘fill_circular_chromosomes’:
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
       fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                      ^
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c: In function ‘genome_write_memory’:
genome-write.c:642:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:642:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c:645:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:645:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome-write.c: In function ‘Genome_write’:
genome-write.c:787:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
   fprintf(stderr,"Genome length is %lu nt\n",genomelength);
                  ^
mv -f .deps/gmap-genome-write.Tpo .deps/gmap-genome-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bitpack64-read.o -MD -MP -MF .deps/gmap-bitpack64-read.Tpo -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gmap-bitpack64-read.Tpo .deps/gmap-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb.o -MD -MP -MF .deps/gmap-indexdb.Tpo -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb_hr.o -MD -MP -MF .deps/gmap-indexdb_hr.Tpo -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligo.o -MD -MP -MF .deps/gmap-oligo.Tpo -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gmap-oligo.Tpo .deps/gmap-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-block.o -MD -MP -MF .deps/gmap-block.Tpo -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c
mv -f .deps/gmap-block.Tpo .deps/gmap-block.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrom.o -MD -MP -MF .deps/gmap-chrom.Tpo -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gmap-chrom.Tpo .deps/gmap-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-segmentpos.o -MD -MP -MF .deps/gmap-segmentpos.Tpo -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/gmap-segmentpos.Tpo .deps/gmap-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrnum.o -MD -MP -MF .deps/gmap-chrnum.Tpo -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gmap-chrnum.Tpo .deps/gmap-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrsubset.o -MD -MP -MF .deps/gmap-chrsubset.Tpo -c -o gmap-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c
mv -f .deps/gmap-chrsubset.Tpo .deps/gmap-chrsubset.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uinttable.o -MD -MP -MF .deps/gmap-uinttable.Tpo -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c
mv -f .deps/gmap-uinttable.Tpo .deps/gmap-uinttable.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gregion.o -MD -MP -MF .deps/gmap-gregion.Tpo -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
mv -f .deps/gmap-gregion.Tpo .deps/gmap-gregion.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-match.o -MD -MP -MF .deps/gmap-match.Tpo -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c
mv -f .deps/gmap-match.Tpo .deps/gmap-match.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-matchpool.o -MD -MP -MF .deps/gmap-matchpool.Tpo -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
mv -f .deps/gmap-matchpool.Tpo .deps/gmap-matchpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagnostic.o -MD -MP -MF .deps/gmap-diagnostic.Tpo -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
mv -f .deps/gmap-diagnostic.Tpo .deps/gmap-diagnostic.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage1.o -MD -MP -MF .deps/gmap-stage1.Tpo -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
mv -f .deps/gmap-stage1.Tpo .deps/gmap-stage1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diag.o -MD -MP -MF .deps/gmap-diag.Tpo -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gmap-diag.Tpo .deps/gmap-diag.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagpool.o -MD -MP -MF .deps/gmap-diagpool.Tpo -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gmap-diagpool.Tpo .deps/gmap-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cmet.o -MD -MP -MF .deps/gmap-cmet.Tpo -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gmap-cmet.Tpo .deps/gmap-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-atoi.o -MD -MP -MF .deps/gmap-atoi.Tpo -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gmap-atoi.Tpo .deps/gmap-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-orderstat.o -MD -MP -MF .deps/gmap-orderstat.Tpo -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gmap-orderstat.Tpo .deps/gmap-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex_hr.o -MD -MP -MF .deps/gmap-oligoindex_hr.Tpo -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gmap-oligoindex_hr.Tpo .deps/gmap-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intron.o -MD -MP -MF .deps/gmap-intron.Tpo -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gmap-intron.Tpo .deps/gmap-intron.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent.o -MD -MP -MF .deps/gmap-maxent.Tpo -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gmap-maxent.Tpo .deps/gmap-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent_hr.o -MD -MP -MF .deps/gmap-maxent_hr.Tpo -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gmap-maxent_hr.Tpo .deps/gmap-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pair.o -MD -MP -MF .deps/gmap-pair.Tpo -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c
mv -f .deps/gmap-pair.Tpo .deps/gmap-pair.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pairpool.o -MD -MP -MF .deps/gmap-pairpool.Tpo -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gmap-pairpool.Tpo .deps/gmap-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cellpool.o -MD -MP -MF .deps/gmap-cellpool.Tpo -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/gmap-cellpool.Tpo .deps/gmap-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage2.o -MD -MP -MF .deps/gmap-stage2.Tpo -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
mv -f .deps/gmap-stage2.Tpo .deps/gmap-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-doublelist.o -MD -MP -MF .deps/gmap-doublelist.Tpo -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/gmap-doublelist.Tpo .deps/gmap-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-smooth.o -MD -MP -MF .deps/gmap-smooth.Tpo -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gmap-smooth.Tpo .deps/gmap-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicestringpool.o -MD -MP -MF .deps/gmap-splicestringpool.Tpo -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/gmap-splicestringpool.Tpo .deps/gmap-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie_build.o -MD -MP -MF .deps/gmap-splicetrie_build.Tpo -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
mv -f .deps/gmap-splicetrie_build.Tpo .deps/gmap-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie.o -MD -MP -MF .deps/gmap-splicetrie.Tpo -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gmap-splicetrie.Tpo .deps/gmap-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-boyer-moore.o -MD -MP -MF .deps/gmap-boyer-moore.Tpo -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gmap-boyer-moore.Tpo .deps/gmap-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-dynprog.o -MD -MP -MF .deps/gmap-dynprog.Tpo -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gmap-dynprog.Tpo .deps/gmap-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-translation.o -MD -MP -MF .deps/gmap-translation.Tpo -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gmap-translation.Tpo .deps/gmap-translation.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pbinom.o -MD -MP -MF .deps/gmap-pbinom.Tpo -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gmap-pbinom.Tpo .deps/gmap-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-changepoint.o -MD -MP -MF .deps/gmap-changepoint.Tpo -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gmap-changepoint.Tpo .deps/gmap-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage3.o -MD -MP -MF .deps/gmap-stage3.Tpo -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gmap-stage3.Tpo .deps/gmap-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-request.o -MD -MP -MF .deps/gmap-request.Tpo -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gmap-request.Tpo .deps/gmap-request.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-result.o -MD -MP -MF .deps/gmap-result.Tpo -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c
mv -f .deps/gmap-result.Tpo .deps/gmap-result.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-inbuffer.o -MD -MP -MF .deps/gmap-inbuffer.Tpo -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gmap-inbuffer.Tpo .deps/gmap-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-samheader.o -MD -MP -MF .deps/gmap-samheader.Tpo -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gmap-samheader.Tpo .deps/gmap-samheader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-outbuffer.o -MD -MP -MF .deps/gmap-outbuffer.Tpo -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gmap-outbuffer.Tpo .deps/gmap-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chimera.o -MD -MP -MF .deps/gmap-chimera.Tpo -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gmap-chimera.Tpo .deps/gmap-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-datadir.o -MD -MP -MF .deps/gmap-datadir.Tpo -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gmap-datadir.Tpo .deps/gmap-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt.o -MD -MP -MF .deps/gmap-getopt.Tpo -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gmap-getopt.Tpo .deps/gmap-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt1.o -MD -MP -MF .deps/gmap-getopt1.Tpo -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gmap-getopt1.Tpo .deps/gmap-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gmap.o -MD -MP -MF .deps/gmap-gmap.Tpo -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
gmap.c: In function ‘apply_stage3’:
gmap.c:3244:28: warning: passing argument 11 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types]
         matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
                            ^
gmap.c:2669:1: note: expected ‘Cellpool_T {aka struct Cellpool_T *}’ but argument is of type ‘Diagpool_T {aka struct Diagpool_T *}’
 check_middle_piece_local (bool *foundp, List_T stage3list, Sequence_T queryseq,
 ^
gmap.c:3244:37: warning: passing argument 12 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types]
         matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
                                     ^
gmap.c:2669:1: note: expected ‘Diagpool_T {aka struct Diagpool_T *}’ but argument is of type ‘Cellpool_T {aka struct Cellpool_T *}’
 check_middle_piece_local (bool *foundp, List_T stage3list, Sequence_T queryseq,
 ^
mv -f .deps/gmap-gmap.Tpo .deps/gmap-gmap.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3    -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o  -lz -lbz2 -lm 
libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-except.o -MD -MP -MF .deps/gmapl-except.Tpo -c -o gmapl-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmapl-except.Tpo .deps/gmapl-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-assert.o -MD -MP -MF .deps/gmapl-assert.Tpo -c -o gmapl-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmapl-assert.Tpo .deps/gmapl-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-mem.o -MD -MP -MF .deps/gmapl-mem.Tpo -c -o gmapl-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmapl-mem.Tpo .deps/gmapl-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intlist.o -MD -MP -MF .deps/gmapl-intlist.Tpo -c -o gmapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmapl-intlist.Tpo .deps/gmapl-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-list.o -MD -MP -MF .deps/gmapl-list.Tpo -c -o gmapl-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmapl-list.Tpo .deps/gmapl-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-littleendian.o -MD -MP -MF .deps/gmapl-littleendian.Tpo -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/gmapl-littleendian.Tpo .deps/gmapl-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bigendian.o -MD -MP -MF .deps/gmapl-bigendian.Tpo -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/gmapl-bigendian.Tpo .deps/gmapl-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-univinterval.o -MD -MP -MF .deps/gmapl-univinterval.Tpo -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/gmapl-univinterval.Tpo .deps/gmapl-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-interval.o -MD -MP -MF .deps/gmapl-interval.Tpo -c -o gmapl-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmapl-interval.Tpo .deps/gmapl-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uintlist.o -MD -MP -MF .deps/gmapl-uintlist.Tpo -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmapl-uintlist.Tpo .deps/gmapl-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stopwatch.o -MD -MP -MF .deps/gmapl-stopwatch.Tpo -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmapl-stopwatch.Tpo .deps/gmapl-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-access.o -MD -MP -MF .deps/gmapl-access.Tpo -c -o gmapl-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/gmapl-access.Tpo .deps/gmapl-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read-univ.o -MD -MP -MF .deps/gmapl-iit-read-univ.Tpo -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/gmapl-iit-read-univ.Tpo .deps/gmapl-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read.o -MD -MP -MF .deps/gmapl-iit-read.Tpo -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/gmapl-iit-read.Tpo .deps/gmapl-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-md5.o -MD -MP -MF .deps/gmapl-md5.Tpo -c -o gmapl-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gmapl-md5.Tpo .deps/gmapl-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bzip2.o -MD -MP -MF .deps/gmapl-bzip2.Tpo -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gmapl-bzip2.Tpo .deps/gmapl-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-sequence.o -MD -MP -MF .deps/gmapl-sequence.Tpo -c -o gmapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gmapl-sequence.Tpo .deps/gmapl-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-reader.o -MD -MP -MF .deps/gmapl-reader.Tpo -c -o gmapl-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gmapl-reader.Tpo .deps/gmapl-reader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genomicpos.o -MD -MP -MF .deps/gmapl-genomicpos.Tpo -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmapl-genomicpos.Tpo .deps/gmapl-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress.o -MD -MP -MF .deps/gmapl-compress.Tpo -c -o gmapl-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmapl-compress.Tpo .deps/gmapl-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress-write.o -MD -MP -MF .deps/gmapl-compress-write.Tpo -c -o gmapl-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c: In function ‘fill_buffer’:
compress-write.c:73:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
         ^
compress-write.c: In function ‘write_compressed_one’:
compress-write.c:251:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
compress-write.c: In function ‘put_compressed_one’:
compress-write.c:299:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
mv -f .deps/gmapl-compress-write.Tpo .deps/gmapl-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gbuffer.o -MD -MP -MF .deps/gmapl-gbuffer.Tpo -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gmapl-gbuffer.Tpo .deps/gmapl-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome.o -MD -MP -MF .deps/gmapl-genome.Tpo -c -o gmapl-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/gmapl-genome.Tpo .deps/gmapl-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_hr.o -MD -MP -MF .deps/gmapl-genome_hr.Tpo -c -o gmapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gmapl-genome_hr.Tpo .deps/gmapl-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_sites.o -MD -MP -MF .deps/gmapl-genome_sites.Tpo -c -o gmapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
genome_sites.c: In function ‘Genome_print_blocks’:
genome_sites.c:24729:10: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%u\t",startblock/3*32U);
          ^
genome_sites.c:24744:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%u\t",ptr/3*32U);
            ^
genome_sites.c:24751:10: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%u\t",(endblock+3)/3*32U);
          ^
mv -f .deps/gmapl-genome_sites.Tpo .deps/gmapl-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome-write.o -MD -MP -MF .deps/gmapl-genome-write.Tpo -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
genome-write.c: In function ‘genome_write_file’:
genome-write.c:252:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:252:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:255:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:255:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c: In function ‘genome_writeraw_file’:
genome-write.c:429:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:429:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:432:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:432:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c: In function ‘fill_circular_chromosomes’:
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                      ^
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c: In function ‘genome_write_memory’:
genome-write.c:642:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:642:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:645:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:645:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c: In function ‘Genome_write’:
genome-write.c:787:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(stderr,"Genome length is %lu nt\n",genomelength);
                  ^
mv -f .deps/gmapl-genome-write.Tpo .deps/gmapl-genome-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bitpack64-read.o -MD -MP -MF .deps/gmapl-bitpack64-read.Tpo -c -o gmapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gmapl-bitpack64-read.Tpo .deps/gmapl-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb.o -MD -MP -MF .deps/gmapl-indexdb.Tpo -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gmapl-indexdb.Tpo .deps/gmapl-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb_hr.o -MD -MP -MF .deps/gmapl-indexdb_hr.Tpo -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘Compoundpos_dump’:
indexdb_hr.c:1008:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm);
              ^
indexdb_hr.c: In function ‘heap_even_dump’:
indexdb_hr.c:1232:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("#%d--%d:%u  ",i,batch->nentries,batch->position);
            ^
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gmapl-indexdb_hr.Tpo .deps/gmapl-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligo.o -MD -MP -MF .deps/gmapl-oligo.Tpo -c -o gmapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gmapl-oligo.Tpo .deps/gmapl-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-block.o -MD -MP -MF .deps/gmapl-block.Tpo -c -o gmapl-block.o `test -f 'block.c' || echo './'`block.c
mv -f .deps/gmapl-block.Tpo .deps/gmapl-block.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrom.o -MD -MP -MF .deps/gmapl-chrom.Tpo -c -o gmapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gmapl-chrom.Tpo .deps/gmapl-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-segmentpos.o -MD -MP -MF .deps/gmapl-segmentpos.Tpo -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
segmentpos.c: In function ‘Segmentpos_print’:
segmentpos.c:90:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length);
              ^
mv -f .deps/gmapl-segmentpos.Tpo .deps/gmapl-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrnum.o -MD -MP -MF .deps/gmapl-chrnum.Tpo -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gmapl-chrnum.Tpo .deps/gmapl-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrsubset.o -MD -MP -MF .deps/gmapl-chrsubset.Tpo -c -o gmapl-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c
mv -f .deps/gmapl-chrsubset.Tpo .deps/gmapl-chrsubset.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uinttable.o -MD -MP -MF .deps/gmapl-uinttable.Tpo -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c
mv -f .deps/gmapl-uinttable.Tpo .deps/gmapl-uinttable.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gregion.o -MD -MP -MF .deps/gmapl-gregion.Tpo -c -o gmapl-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
mv -f .deps/gmapl-gregion.Tpo .deps/gmapl-gregion.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-match.o -MD -MP -MF .deps/gmapl-match.Tpo -c -o gmapl-match.o `test -f 'match.c' || echo './'`match.c
mv -f .deps/gmapl-match.Tpo .deps/gmapl-match.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-matchpool.o -MD -MP -MF .deps/gmapl-matchpool.Tpo -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
mv -f .deps/gmapl-matchpool.Tpo .deps/gmapl-matchpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagnostic.o -MD -MP -MF .deps/gmapl-diagnostic.Tpo -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
mv -f .deps/gmapl-diagnostic.Tpo .deps/gmapl-diagnostic.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage1.o -MD -MP -MF .deps/gmapl-stage1.Tpo -c -o gmapl-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
mv -f .deps/gmapl-stage1.Tpo .deps/gmapl-stage1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diag.o -MD -MP -MF .deps/gmapl-diag.Tpo -c -o gmapl-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gmapl-diag.Tpo .deps/gmapl-diag.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagpool.o -MD -MP -MF .deps/gmapl-diagpool.Tpo -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gmapl-diagpool.Tpo .deps/gmapl-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cmet.o -MD -MP -MF .deps/gmapl-cmet.Tpo -c -o gmapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gmapl-cmet.Tpo .deps/gmapl-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-atoi.o -MD -MP -MF .deps/gmapl-atoi.Tpo -c -o gmapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gmapl-atoi.Tpo .deps/gmapl-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-orderstat.o -MD -MP -MF .deps/gmapl-orderstat.Tpo -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gmapl-orderstat.Tpo .deps/gmapl-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligoindex_hr.o -MD -MP -MF .deps/gmapl-oligoindex_hr.Tpo -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gmapl-oligoindex_hr.Tpo .deps/gmapl-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intron.o -MD -MP -MF .deps/gmapl-intron.Tpo -c -o gmapl-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gmapl-intron.Tpo .deps/gmapl-intron.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent.o -MD -MP -MF .deps/gmapl-maxent.Tpo -c -o gmapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gmapl-maxent.Tpo .deps/gmapl-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent_hr.o -MD -MP -MF .deps/gmapl-maxent_hr.Tpo -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gmapl-maxent_hr.Tpo .deps/gmapl-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pair.o -MD -MP -MF .deps/gmapl-pair.Tpo -c -o gmapl-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c: In function ‘print_genomic_sequence’:
pair.c:546:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘print_genomicalt_sequence’:
pair.c:573:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘compute_margin’:
pair.c:600:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP);
                    ^
pair.c:607:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘Pair_print_coordinates’:
pair.c:1272:13: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(fp,"%u %u %c",this->genomepos + ONEBASEDP,
             ^
pair.c:1276:13: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(fp,"%s:%u %u %c",chrstring,
             ^
pair.c: In function ‘Pair_print_exonsummary’:
pair.c:1790:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                 ^
pair.c:1790:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1799:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                 ^
pair.c:1799:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1913:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ^
pair.c:1913:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1922:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ^
pair.c:1922:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c: In function ‘Pair_print_compressed’:
pair.c:6986:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
              ^
pair.c:6986:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/gmapl-pair.Tpo .deps/gmapl-pair.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pairpool.o -MD -MP -MF .deps/gmapl-pairpool.Tpo -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gmapl-pairpool.Tpo .deps/gmapl-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cellpool.o -MD -MP -MF .deps/gmapl-cellpool.Tpo -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/gmapl-cellpool.Tpo .deps/gmapl-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage2.o -MD -MP -MF .deps/gmapl-stage2.Tpo -c -o gmapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
mv -f .deps/gmapl-stage2.Tpo .deps/gmapl-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-doublelist.o -MD -MP -MF .deps/gmapl-doublelist.Tpo -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/gmapl-doublelist.Tpo .deps/gmapl-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-smooth.o -MD -MP -MF .deps/gmapl-smooth.Tpo -c -o gmapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gmapl-smooth.Tpo .deps/gmapl-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicestringpool.o -MD -MP -MF .deps/gmapl-splicestringpool.Tpo -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/gmapl-splicestringpool.Tpo .deps/gmapl-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie_build.o -MD -MP -MF .deps/gmapl-splicetrie_build.Tpo -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
splicetrie_build.c: In function ‘Splicetrie_dump’:
splicetrie_build.c:132:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%d %u",(int) leaf,position);
            ^
splicetrie_build.c:146:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%d %u",(int) leaf,position);
              ^
mv -f .deps/gmapl-splicetrie_build.Tpo .deps/gmapl-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie.o -MD -MP -MF .deps/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gmapl-splicetrie.Tpo .deps/gmapl-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-boyer-moore.o -MD -MP -MF .deps/gmapl-boyer-moore.Tpo -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gmapl-boyer-moore.Tpo .deps/gmapl-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-dynprog.o -MD -MP -MF .deps/gmapl-dynprog.Tpo -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gmapl-dynprog.Tpo .deps/gmapl-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-translation.o -MD -MP -MF .deps/gmapl-translation.Tpo -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gmapl-translation.Tpo .deps/gmapl-translation.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pbinom.o -MD -MP -MF .deps/gmapl-pbinom.Tpo -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gmapl-pbinom.Tpo .deps/gmapl-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-changepoint.o -MD -MP -MF .deps/gmapl-changepoint.Tpo -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gmapl-changepoint.Tpo .deps/gmapl-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage3.o -MD -MP -MF .deps/gmapl-stage3.Tpo -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gmapl-stage3.Tpo .deps/gmapl-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-request.o -MD -MP -MF .deps/gmapl-request.Tpo -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gmapl-request.Tpo .deps/gmapl-request.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-result.o -MD -MP -MF .deps/gmapl-result.Tpo -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c
mv -f .deps/gmapl-result.Tpo .deps/gmapl-result.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-inbuffer.o -MD -MP -MF .deps/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gmapl-inbuffer.Tpo .deps/gmapl-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-samheader.o -MD -MP -MF .deps/gmapl-samheader.Tpo -c -o gmapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gmapl-samheader.Tpo .deps/gmapl-samheader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-outbuffer.o -MD -MP -MF .deps/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gmapl-outbuffer.Tpo .deps/gmapl-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chimera.o -MD -MP -MF .deps/gmapl-chimera.Tpo -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gmapl-chimera.Tpo .deps/gmapl-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-datadir.o -MD -MP -MF .deps/gmapl-datadir.Tpo -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gmapl-datadir.Tpo .deps/gmapl-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt.o -MD -MP -MF .deps/gmapl-getopt.Tpo -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gmapl-getopt.Tpo .deps/gmapl-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt1.o -MD -MP -MF .deps/gmapl-getopt1.Tpo -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gmapl-getopt1.Tpo .deps/gmapl-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gmap.o -MD -MP -MF .deps/gmapl-gmap.Tpo -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
gmap.c: In function ‘apply_stage3’:
gmap.c:3244:28: warning: passing argument 11 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types]
         matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
                            ^
gmap.c:2669:1: note: expected ‘Cellpool_T {aka struct Cellpool_T *}’ but argument is of type ‘Diagpool_T {aka struct Diagpool_T *}’
 check_middle_piece_local (bool *foundp, List_T stage3list, Sequence_T queryseq,
 ^
gmap.c:3244:37: warning: passing argument 12 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types]
         matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
                                     ^
gmap.c:2669:1: note: expected ‘Diagpool_T {aka struct Diagpool_T *}’ but argument is of type ‘Cellpool_T {aka struct Cellpool_T *}’
 check_middle_piece_local (bool *foundp, List_T stage3list, Sequence_T queryseq,
 ^
mv -f .deps/gmapl-gmap.Tpo .deps/gmapl-gmap.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3    -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o  -lz -lbz2 -lm 
libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-except.o -MD -MP -MF .deps/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/get_genome-except.Tpo .deps/get_genome-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-assert.o -MD -MP -MF .deps/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/get_genome-assert.Tpo .deps/get_genome-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-mem.o -MD -MP -MF .deps/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-intlist.o -MD -MP -MF .deps/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-list.o -MD -MP -MF .deps/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/get_genome-list.Tpo .deps/get_genome-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-littleendian.o -MD -MP -MF .deps/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bigendian.o -MD -MP -MF .deps/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-univinterval.o -MD -MP -MF .deps/get_genome-univinterval.Tpo -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/get_genome-univinterval.Tpo .deps/get_genome-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-interval.o -MD -MP -MF .deps/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/get_genome-interval.Tpo .deps/get_genome-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-stopwatch.o -MD -MP -MF .deps/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/get_genome-stopwatch.Tpo .deps/get_genome-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-access.o -MD -MP -MF .deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read-univ.o -MD -MP -MF .deps/get_genome-iit-read-univ.Tpo -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read.o -MD -MP -MF .deps/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-md5.o -MD -MP -MF .deps/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bzip2.o -MD -MP -MF .deps/get_genome-bzip2.Tpo -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/get_genome-bzip2.Tpo .deps/get_genome-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genome.o -MD -MP -MF .deps/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genomicpos.o -MD -MP -MF .deps/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrom.o -MD -MP -MF .deps/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrnum.o -MD -MP -MF .deps/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/get_genome-chrnum.Tpo .deps/get_genome-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrsubset.o -MD -MP -MF .deps/get_genome-chrsubset.Tpo -c -o get_genome-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c
mv -f .deps/get_genome-chrsubset.Tpo .deps/get_genome-chrsubset.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-datadir.o -MD -MP -MF .deps/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-parserange.o -MD -MP -MF .deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
parserange.c: In function ‘translate_chromosomepos_universal’:
parserange.c:186:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n",
                      ^
parserange.c:186:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
parserange.c:186:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt.o -MD -MP -MF .deps/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/get_genome-getopt.Tpo .deps/get_genome-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt1.o -MD -MP -MF .deps/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-get-genome.o -MD -MP -MF .deps/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c
get-genome.c: In function ‘print_two_coords’:
get-genome.c:194:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu%s%lu\t",left+1,SEPARATOR,left+length);
          ^
get-genome.c:194:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
get-genome.c: In function ‘print_sequence’:
get-genome.c:410:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf(" %s:%lu%s%lu\n",dbversion,genomicstart+genomiclength,SEPARATOR,genomicstart+1U);
              ^
get-genome.c:410:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
get-genome.c:428:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf(" %s:%lu%s%lu\n",dbversion,genomicstart+1U,SEPARATOR,genomicstart+genomiclength);
              ^
get-genome.c:428:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3    -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o  -lz -lbz2 -lm 
libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-assert.o -MD -MP -MF .deps/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gmapindex-assert.Tpo .deps/gmapindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-list.o -MD -MP -MF .deps/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gmapindex-list.Tpo .deps/gmapindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-univinterval.o -MD -MP -MF .deps/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-uintlist.o -MD -MP -MF .deps/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-stopwatch.o -MD -MP -MF .deps/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-iit-read-univ.o -MD -MP -MF .deps/gmapindex-iit-read-univ.Tpo -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-iit-write-univ.o -MD -MP -MF .deps/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c
mv -f .deps/gmapindex-iit-write-univ.Tpo .deps/gmapindex-iit-write-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-iit-read.o -MD -MP -MF .deps/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-md5.o -MD -MP -MF .deps/gmapindex-md5.Tpo -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gmapindex-md5.Tpo .deps/gmapindex-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-bzip2.o -MD -MP -MF .deps/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gmapindex-bzip2.Tpo .deps/gmapindex-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-sequence.o -MD -MP -MF .deps/gmapindex-sequence.Tpo -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gmapindex-sequence.Tpo .deps/gmapindex-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-genome.o -MD -MP -MF .deps/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-compress-write.o -MD -MP -MF .deps/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c: In function ‘fill_buffer’:
compress-write.c:73:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
         ^
compress-write.c: In function ‘write_compressed_one’:
compress-write.c:251:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
compress-write.c: In function ‘put_compressed_one’:
compress-write.c:299:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
genome-write.c: In function ‘genome_write_file’:
genome-write.c:252:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:252:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:255:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:255:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c: In function ‘genome_writeraw_file’:
genome-write.c:429:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:429:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:432:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:432:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c: In function ‘fill_circular_chromosomes’:
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Chromosome %s is circular.  Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U);
                      ^
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:595:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c: In function ‘genome_write_memory’:
genome-write.c:642:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:642:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c:645:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
    fprintf(stderr,"Writing contig %s to universal coordinates %lu..%lu in genome %s\n",
                   ^
genome-write.c:645:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome-write.c: In function ‘Genome_write’:
genome-write.c:787:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(stderr,"Genome length is %lu nt\n",genomelength);
                  ^
mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-compress.o -MD -MP -MF .deps/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gmapindex-compress.Tpo .deps/gmapindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-genome_hr.o -MD -MP -MF .deps/gmapindex-genome_hr.Tpo -c -o gmapindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gmapindex-genome_hr.Tpo .deps/gmapindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-read.o -MD -MP -MF .deps/gmapindex-bitpack64-read.Tpo -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-write.o -MD -MP -MF .deps/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/gmapindex-bitpack64-write.Tpo .deps/gmapindex-bitpack64-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-indexdb.o -MD -MP -MF .deps/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-indexdb-write.o -MD -MP -MF .deps/gmapindex-indexdb-write.Tpo -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c: In function ‘check_offsets_from_bitpack’:
indexdb-write.c:2494:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u.  Please inform twu@gene.com\n",
                 ^
indexdb-write.c:2494:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
indexdb-write.c:2494:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
indexdb-write.c: In function ‘check_offsets_from_gammas’:
indexdb-write.c:2726:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                      ^
indexdb-write.c:2737:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                      ^
indexdb-write.c:2760:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
  fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                 ^
indexdb-write.c:2787:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                    ^
indexdb-write.c:2798:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                    ^
indexdb-write.c: In function ‘Indexdb_write_offsets’:
indexdb-write.c:2888:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
   fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T));
                  ^
indexdb-write.c:2895:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part);
                    ^
indexdb-write.c:2972:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
indexdb-write.c:3094:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]);
                      ^
indexdb-write.c:3127:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                      ^
indexdb-write.c:3171:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                      ^
indexdb-write.c: In function ‘compute_positions_in_file’:
indexdb-write.c:3371:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
indexdb-write.c: In function ‘compute_positions_in_memory’:
indexdb-write.c:3601:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
mv -f .deps/gmapindex-indexdb-write.Tpo .deps/gmapindex-indexdb-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-table.o -MD -MP -MF .deps/gmapindex-table.Tpo -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c
table.c: In function ‘Table_gc’:
table.c:283:18: warning: passing argument 1 of ‘keyfree’ from incompatible pointer type [-Wincompatible-pointer-types]
       (*keyfree)(&p->key);
                  ^
table.c:283:18: note: expected ‘void **’ but argument is of type ‘const void **’
mv -f .deps/gmapindex-table.Tpo .deps/gmapindex-table.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-tableuint.o -MD -MP -MF .deps/gmapindex-tableuint.Tpo -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c
mv -f .deps/gmapindex-tableuint.Tpo .deps/gmapindex-tableuint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-tableuint8.o -MD -MP -MF .deps/gmapindex-tableuint8.Tpo -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c
mv -f .deps/gmapindex-tableuint8.Tpo .deps/gmapindex-tableuint8.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-chrom.o -MD -MP -MF .deps/gmapindex-chrom.Tpo -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gmapindex-chrom.Tpo .deps/gmapindex-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-segmentpos.o -MD -MP -MF .deps/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
segmentpos.c: In function ‘Segmentpos_print’:
segmentpos.c:90:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length);
              ^
mv -f .deps/gmapindex-segmentpos.Tpo .deps/gmapindex-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-saca-k.o -MD -MP -MF .deps/gmapindex-saca-k.Tpo -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c
mv -f .deps/gmapindex-saca-k.Tpo .deps/gmapindex-saca-k.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-sarray-write.o -MD -MP -MF .deps/gmapindex-sarray-write.Tpo -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c
mv -f .deps/gmapindex-sarray-write.Tpo .deps/gmapindex-sarray-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3 -MT gmapindex-gmapindex.o -MD -MP -MF .deps/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c
gmapindex.c: In function ‘process_sequence_aux’:
gmapindex.c:305:26: warning: format ‘%lu’ expects argument of type ‘long unsigned int *’, but argument 5 has type ‘Univcoord_T * {aka long long unsigned int *}’ [-Wformat=]
   nitems = sscanf(Buffer,"%s %s %lu",accession_p,chrpos_string,&universal_coord);
                          ^
gmapindex.c: In function ‘write_chromosome_file’:
gmapindex.c:509:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Chromosome %s has universal coordinates %lu..%lu\n",
                      ^
gmapindex.c:509:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
gmapindex.c:520:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(textfp,"%s\t%lu..%lu\t%u",
                    ^
gmapindex.c:520:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
gmapindex.c: In function ‘write_contig_file’:
gmapindex.c:695:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(textfp,"%s\t%lu..%lu\t%s:%u..%u\t%u",
                      ^
gmapindex.c:695:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
gmapindex.c:700:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(textfp,"%s\t%lu..%lu\t%s:%u..%u\t%u",
                      ^
gmapindex.c:700:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
gmapindex.c: In function ‘main’:
gmapindex.c:1061:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Total genomic length = %lu bp\n",totalnts);
                    ^
mv -f .deps/gmapindex-gmapindex.Tpo .deps/gmapindex-gmapindex.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DUTILITYP=1 -O3    -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o  -lz -lbz2 -lm 
libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DUTILITYP=1 -O3 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-except.o -MD -MP -MF .deps/iit_store-except.Tpo -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_store-except.Tpo .deps/iit_store-except.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-assert.o -MD -MP -MF .deps/iit_store-assert.Tpo -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_store-assert.Tpo .deps/iit_store-assert.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-mem.o -MD -MP -MF .deps/iit_store-mem.Tpo -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_store-mem.Tpo .deps/iit_store-mem.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-intlist.o -MD -MP -MF .deps/iit_store-intlist.Tpo -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_store-intlist.Tpo .deps/iit_store-intlist.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-list.o -MD -MP -MF .deps/iit_store-list.Tpo -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_store-list.Tpo .deps/iit_store-list.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-littleendian.o -MD -MP -MF .deps/iit_store-littleendian.Tpo -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/iit_store-littleendian.Tpo .deps/iit_store-littleendian.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-bigendian.o -MD -MP -MF .deps/iit_store-bigendian.Tpo -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/iit_store-bigendian.Tpo .deps/iit_store-bigendian.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-univinterval.o -MD -MP -MF .deps/iit_store-univinterval.Tpo -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/iit_store-univinterval.Tpo .deps/iit_store-univinterval.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-interval.o -MD -MP -MF .deps/iit_store-interval.Tpo -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_store-interval.Tpo .deps/iit_store-interval.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-uintlist.o -MD -MP -MF .deps/iit_store-uintlist.Tpo -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_store-uintlist.Tpo .deps/iit_store-uintlist.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-stopwatch.o -MD -MP -MF .deps/iit_store-stopwatch.Tpo -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_store-stopwatch.Tpo .deps/iit_store-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-access.o -MD -MP -MF .deps/iit_store-access.Tpo -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/iit_store-access.Tpo .deps/iit_store-access.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-iit-write-univ.o -MD -MP -MF .deps/iit_store-iit-write-univ.Tpo -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c
mv -f .deps/iit_store-iit-write-univ.Tpo .deps/iit_store-iit-write-univ.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-iit-write.o -MD -MP -MF .deps/iit_store-iit-write.Tpo -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c
mv -f .deps/iit_store-iit-write.Tpo .deps/iit_store-iit-write.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-tableint.o -MD -MP -MF .deps/iit_store-tableint.Tpo -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c
mv -f .deps/iit_store-tableint.Tpo .deps/iit_store-tableint.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-table.o -MD -MP -MF .deps/iit_store-table.Tpo -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c
table.c: In function ‘Table_gc’:
table.c:283:18: warning: passing argument 1 of ‘keyfree’ from incompatible pointer type [-Wincompatible-pointer-types]
       (*keyfree)(&p->key);
                  ^
table.c:283:18: note: expected ‘void **’ but argument is of type ‘const void **’
mv -f .deps/iit_store-table.Tpo .deps/iit_store-table.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-chrom.o -MD -MP -MF .deps/iit_store-chrom.Tpo -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/iit_store-chrom.Tpo .deps/iit_store-chrom.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-getopt.o -MD -MP -MF .deps/iit_store-getopt.Tpo -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_store-getopt.Tpo .deps/iit_store-getopt.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-getopt1.o -MD -MP -MF .deps/iit_store-getopt1.Tpo -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_store-getopt1.Tpo .deps/iit_store-getopt1.Po
gcc -DHAVE_CONFIG_H -I.      -pthread -DUTILITYP=1 -O3 -MT iit_store-iit_store.o -MD -MP -MF .deps/iit_store-iit_store.Tpo -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c
iit_store.c: In function ‘scan_header_spaces’:
iit_store.c:371:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int *’, but argument 4 has type ‘Univcoord_T * {aka long long unsigned int *}’ [-Wformat=]
   nscanned = sscanf(header,">%s %lu %lu\n",Buffer,&(*start),&(*end));
                            ^
iit_store.c:371:28: warning: format ‘%lu’ expects argument of type ‘long unsigned int *’, but argument 5 has type ‘Univcoord_T * {aka long long unsigned int *}’ [-Wformat=]
iit_store.c: In function ‘parse_fasta’:
iit_store.c:596:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(stderr,"Maximum coordinate: %lu\n",*max_coordinate);
                  ^
iit_store.c:597:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(stderr,"Total label length: %lu + %d separators\n",*label_totallength,nentries);
                  ^
iit_store.c:598:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(stderr,"Total annotation length: %lu + %d separators\n",*annot_totallength,nentries);
                  ^
iit_store.c: In function ‘parse_fieldlist’:
iit_store.c:447:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
       fgets(&(Buffer[1]),LINELENGTH-1,fp);
       ^
iit_store.c: In function ‘parse_fasta’:
iit_store.c:482:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(Buffer,LINELENGTH,fp);
     ^
iit_store.c:485:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(&(Buffer[1]),LINELENGTH-1,fp);
     ^
mv -f .deps/iit_store-iit_store.Tpo .deps/iit_store-iit_store.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc   -pthread -DUTILITYP=1 -O3    -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o  -lm 
libtool: link: gcc -pthread -DUTILITYP=1 -O3 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-except.o -MD -MP -MF .deps/iit_get-except.Tpo -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_get-except.Tpo .deps/iit_get-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-assert.o -MD -MP -MF .deps/iit_get-assert.Tpo -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_get-assert.Tpo .deps/iit_get-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-mem.o -MD -MP -MF .deps/iit_get-mem.Tpo -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_get-mem.Tpo .deps/iit_get-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-intlist.o -MD -MP -MF .deps/iit_get-intlist.Tpo -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_get-intlist.Tpo .deps/iit_get-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-list.o -MD -MP -MF .deps/iit_get-list.Tpo -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_get-list.Tpo .deps/iit_get-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-littleendian.o -MD -MP -MF .deps/iit_get-littleendian.Tpo -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/iit_get-littleendian.Tpo .deps/iit_get-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-bigendian.o -MD -MP -MF .deps/iit_get-bigendian.Tpo -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/iit_get-bigendian.Tpo .deps/iit_get-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-univinterval.o -MD -MP -MF .deps/iit_get-univinterval.Tpo -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/iit_get-univinterval.Tpo .deps/iit_get-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-interval.o -MD -MP -MF .deps/iit_get-interval.Tpo -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_get-interval.Tpo .deps/iit_get-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-uintlist.o -MD -MP -MF .deps/iit_get-uintlist.Tpo -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_get-uintlist.Tpo .deps/iit_get-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-stopwatch.o -MD -MP -MF .deps/iit_get-stopwatch.Tpo -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_get-stopwatch.Tpo .deps/iit_get-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-access.o -MD -MP -MF .deps/iit_get-access.Tpo -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/iit_get-access.Tpo .deps/iit_get-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-iit-read-univ.o -MD -MP -MF .deps/iit_get-iit-read-univ.Tpo -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/iit_get-iit-read-univ.Tpo .deps/iit_get-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-iit-read.o -MD -MP -MF .deps/iit_get-iit-read.Tpo -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/iit_get-iit-read.Tpo .deps/iit_get-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-parserange.o -MD -MP -MF .deps/iit_get-parserange.Tpo -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c
parserange.c: In function ‘translate_chromosomepos_universal’:
parserange.c:186:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n",
                      ^
parserange.c:186:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
parserange.c:186:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/iit_get-parserange.Tpo .deps/iit_get-parserange.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-getopt.o -MD -MP -MF .deps/iit_get-getopt.Tpo -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_get-getopt.Tpo .deps/iit_get-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-getopt1.o -MD -MP -MF .deps/iit_get-getopt1.Tpo -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_get-getopt1.Tpo .deps/iit_get-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_get-iit_get.o -MD -MP -MF .deps/iit_get-iit_get.Tpo -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c
iit_get.c: In function ‘print_interval_univ’:
iit_get.c:619:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu",Univinterval_low(interval),Univinterval_high(interval));
            ^
iit_get.c:619:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/iit_get-iit_get.Tpo .deps/iit_get-iit_get.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -DUTILITYP=1 -O3    -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o  -lm 
libtool: link: gcc -pthread -DUTILITYP=1 -O3 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-except.o -MD -MP -MF .deps/iit_dump-except.Tpo -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/iit_dump-except.Tpo .deps/iit_dump-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-assert.o -MD -MP -MF .deps/iit_dump-assert.Tpo -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/iit_dump-assert.Tpo .deps/iit_dump-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-mem.o -MD -MP -MF .deps/iit_dump-mem.Tpo -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/iit_dump-mem.Tpo .deps/iit_dump-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-littleendian.o -MD -MP -MF .deps/iit_dump-littleendian.Tpo -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/iit_dump-littleendian.Tpo .deps/iit_dump-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-bigendian.o -MD -MP -MF .deps/iit_dump-bigendian.Tpo -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/iit_dump-bigendian.Tpo .deps/iit_dump-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-intlist.o -MD -MP -MF .deps/iit_dump-intlist.Tpo -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/iit_dump-intlist.Tpo .deps/iit_dump-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-list.o -MD -MP -MF .deps/iit_dump-list.Tpo -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/iit_dump-list.Tpo .deps/iit_dump-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-univinterval.o -MD -MP -MF .deps/iit_dump-univinterval.Tpo -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/iit_dump-univinterval.Tpo .deps/iit_dump-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-interval.o -MD -MP -MF .deps/iit_dump-interval.Tpo -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/iit_dump-interval.Tpo .deps/iit_dump-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-uintlist.o -MD -MP -MF .deps/iit_dump-uintlist.Tpo -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/iit_dump-uintlist.Tpo .deps/iit_dump-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-stopwatch.o -MD -MP -MF .deps/iit_dump-stopwatch.Tpo -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/iit_dump-stopwatch.Tpo .deps/iit_dump-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-access.o -MD -MP -MF .deps/iit_dump-access.Tpo -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/iit_dump-access.Tpo .deps/iit_dump-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-iit-read-univ.o -MD -MP -MF .deps/iit_dump-iit-read-univ.Tpo -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/iit_dump-iit-read-univ.Tpo .deps/iit_dump-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-iit-read.o -MD -MP -MF .deps/iit_dump-iit-read.Tpo -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/iit_dump-iit-read.Tpo .deps/iit_dump-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-getopt.o -MD -MP -MF .deps/iit_dump-getopt.Tpo -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/iit_dump-getopt.Tpo .deps/iit_dump-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-getopt1.o -MD -MP -MF .deps/iit_dump-getopt1.Tpo -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/iit_dump-getopt1.Tpo .deps/iit_dump-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DUTILITYP=1 -O3 -MT iit_dump-iit_dump.o -MD -MP -MF .deps/iit_dump-iit_dump.Tpo -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c
mv -f .deps/iit_dump-iit_dump.Tpo .deps/iit_dump-iit_dump.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -DUTILITYP=1 -O3    -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o  -lm 
libtool: link: gcc -pthread -DUTILITYP=1 -O3 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-except.o -MD -MP -MF .deps/gsnap-except.Tpo -c -o gsnap-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gsnap-except.Tpo .deps/gsnap-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-assert.o -MD -MP -MF .deps/gsnap-assert.Tpo -c -o gsnap-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gsnap-assert.Tpo .deps/gsnap-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mem.o -MD -MP -MF .deps/gsnap-mem.Tpo -c -o gsnap-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gsnap-mem.Tpo .deps/gsnap-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intlist.o -MD -MP -MF .deps/gsnap-intlist.Tpo -c -o gsnap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gsnap-intlist.Tpo .deps/gsnap-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-list.o -MD -MP -MF .deps/gsnap-list.Tpo -c -o gsnap-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gsnap-list.Tpo .deps/gsnap-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-littleendian.o -MD -MP -MF .deps/gsnap-littleendian.Tpo -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/gsnap-littleendian.Tpo .deps/gsnap-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bigendian.o -MD -MP -MF .deps/gsnap-bigendian.Tpo -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/gsnap-bigendian.Tpo .deps/gsnap-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-univinterval.o -MD -MP -MF .deps/gsnap-univinterval.Tpo -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
mv -f .deps/gsnap-univinterval.Tpo .deps/gsnap-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-interval.o -MD -MP -MF .deps/gsnap-interval.Tpo -c -o gsnap-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gsnap-interval.Tpo .deps/gsnap-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-uintlist.o -MD -MP -MF .deps/gsnap-uintlist.Tpo -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gsnap-uintlist.Tpo .deps/gsnap-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stopwatch.o -MD -MP -MF .deps/gsnap-stopwatch.Tpo -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gsnap-stopwatch.Tpo .deps/gsnap-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-access.o -MD -MP -MF .deps/gsnap-access.Tpo -c -o gsnap-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/gsnap-access.Tpo .deps/gsnap-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read-univ.o -MD -MP -MF .deps/gsnap-iit-read-univ.Tpo -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/gsnap-iit-read-univ.Tpo .deps/gsnap-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read.o -MD -MP -MF .deps/gsnap-iit-read.Tpo -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/gsnap-iit-read.Tpo .deps/gsnap-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-md5.o -MD -MP -MF .deps/gsnap-md5.Tpo -c -o gsnap-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gsnap-md5.Tpo .deps/gsnap-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bzip2.o -MD -MP -MF .deps/gsnap-bzip2.Tpo -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gsnap-bzip2.Tpo .deps/gsnap-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sequence.o -MD -MP -MF .deps/gsnap-sequence.Tpo -c -o gsnap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gsnap-sequence.Tpo .deps/gsnap-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-reader.o -MD -MP -MF .deps/gsnap-reader.Tpo -c -o gsnap-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gsnap-reader.Tpo .deps/gsnap-reader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genomicpos.o -MD -MP -MF .deps/gsnap-genomicpos.Tpo -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gsnap-genomicpos.Tpo .deps/gsnap-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-compress.o -MD -MP -MF .deps/gsnap-compress.Tpo -c -o gsnap-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gsnap-compress.Tpo .deps/gsnap-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome.o -MD -MP -MF .deps/gsnap-genome.Tpo -c -o gsnap-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/gsnap-genome.Tpo .deps/gsnap-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_hr.o -MD -MP -MF .deps/gsnap-genome_hr.Tpo -c -o gsnap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gsnap-genome_hr.Tpo .deps/gsnap-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_sites.o -MD -MP -MF .deps/gsnap-genome_sites.Tpo -c -o gsnap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
mv -f .deps/gsnap-genome_sites.Tpo .deps/gsnap-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-read.o -MD -MP -MF .deps/gsnap-bitpack64-read.Tpo -c -o gsnap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gsnap-bitpack64-read.Tpo .deps/gsnap-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb.o -MD -MP -MF .deps/gsnap-indexdb.Tpo -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gsnap-indexdb.Tpo .deps/gsnap-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb_hr.o -MD -MP -MF .deps/gsnap-indexdb_hr.Tpo -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gsnap-indexdb_hr.Tpo .deps/gsnap-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligo.o -MD -MP -MF .deps/gsnap-oligo.Tpo -c -o gsnap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gsnap-oligo.Tpo .deps/gsnap-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrom.o -MD -MP -MF .deps/gsnap-chrom.Tpo -c -o gsnap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gsnap-chrom.Tpo .deps/gsnap-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-segmentpos.o -MD -MP -MF .deps/gsnap-segmentpos.Tpo -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/gsnap-segmentpos.Tpo .deps/gsnap-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrnum.o -MD -MP -MF .deps/gsnap-chrnum.Tpo -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gsnap-chrnum.Tpo .deps/gsnap-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent_hr.o -MD -MP -MF .deps/gsnap-maxent_hr.Tpo -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gsnap-maxent_hr.Tpo .deps/gsnap-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samprint.o -MD -MP -MF .deps/gsnap-samprint.Tpo -c -o gsnap-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
mv -f .deps/gsnap-samprint.Tpo .deps/gsnap-samprint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mapq.o -MD -MP -MF .deps/gsnap-mapq.Tpo -c -o gsnap-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/gsnap-mapq.Tpo .deps/gsnap-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-shortread.o -MD -MP -MF .deps/gsnap-shortread.Tpo -c -o gsnap-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/gsnap-shortread.Tpo .deps/gsnap-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-substring.o -MD -MP -MF .deps/gsnap-substring.Tpo -c -o gsnap-substring.o `test -f 'substring.c' || echo './'`substring.c
mv -f .deps/gsnap-substring.Tpo .deps/gsnap-substring.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3hr.o -MD -MP -MF .deps/gsnap-stage3hr.Tpo -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/gsnap-stage3hr.Tpo .deps/gsnap-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-goby.o -MD -MP -MF .deps/gsnap-goby.Tpo -c -o gsnap-goby.o `test -f 'goby.c' || echo './'`goby.c
mv -f .deps/gsnap-goby.Tpo .deps/gsnap-goby.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-spanningelt.o -MD -MP -MF .deps/gsnap-spanningelt.Tpo -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/gsnap-spanningelt.Tpo .deps/gsnap-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cmet.o -MD -MP -MF .deps/gsnap-cmet.Tpo -c -o gsnap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gsnap-cmet.Tpo .deps/gsnap-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-atoi.o -MD -MP -MF .deps/gsnap-atoi.Tpo -c -o gsnap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gsnap-atoi.Tpo .deps/gsnap-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent.o -MD -MP -MF .deps/gsnap-maxent.Tpo -c -o gsnap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gsnap-maxent.Tpo .deps/gsnap-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pair.o -MD -MP -MF .deps/gsnap-pair.Tpo -c -o gsnap-pair.o `test -f 'pair.c' || echo './'`pair.c
mv -f .deps/gsnap-pair.Tpo .deps/gsnap-pair.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pairpool.o -MD -MP -MF .deps/gsnap-pairpool.Tpo -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gsnap-pairpool.Tpo .deps/gsnap-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diag.o -MD -MP -MF .deps/gsnap-diag.Tpo -c -o gsnap-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gsnap-diag.Tpo .deps/gsnap-diag.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diagpool.o -MD -MP -MF .deps/gsnap-diagpool.Tpo -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gsnap-diagpool.Tpo .deps/gsnap-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-orderstat.o -MD -MP -MF .deps/gsnap-orderstat.Tpo -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gsnap-orderstat.Tpo .deps/gsnap-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligoindex_hr.o -MD -MP -MF .deps/gsnap-oligoindex_hr.Tpo -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gsnap-oligoindex_hr.Tpo .deps/gsnap-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cellpool.o -MD -MP -MF .deps/gsnap-cellpool.Tpo -c -o gsnap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/gsnap-cellpool.Tpo .deps/gsnap-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage2.o -MD -MP -MF .deps/gsnap-stage2.Tpo -c -o gsnap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
mv -f .deps/gsnap-stage2.Tpo .deps/gsnap-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intron.o -MD -MP -MF .deps/gsnap-intron.Tpo -c -o gsnap-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gsnap-intron.Tpo .deps/gsnap-intron.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-boyer-moore.o -MD -MP -MF .deps/gsnap-boyer-moore.Tpo -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gsnap-boyer-moore.Tpo .deps/gsnap-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-changepoint.o -MD -MP -MF .deps/gsnap-changepoint.Tpo -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gsnap-changepoint.Tpo .deps/gsnap-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pbinom.o -MD -MP -MF .deps/gsnap-pbinom.Tpo -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gsnap-pbinom.Tpo .deps/gsnap-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-dynprog.o -MD -MP -MF .deps/gsnap-dynprog.Tpo -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gsnap-dynprog.Tpo .deps/gsnap-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gbuffer.o -MD -MP -MF .deps/gsnap-gbuffer.Tpo -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gsnap-gbuffer.Tpo .deps/gsnap-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-translation.o -MD -MP -MF .deps/gsnap-translation.Tpo -c -o gsnap-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gsnap-translation.Tpo .deps/gsnap-translation.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-doublelist.o -MD -MP -MF .deps/gsnap-doublelist.Tpo -c -o gsnap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/gsnap-doublelist.Tpo .deps/gsnap-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-smooth.o -MD -MP -MF .deps/gsnap-smooth.Tpo -c -o gsnap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gsnap-smooth.Tpo .deps/gsnap-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chimera.o -MD -MP -MF .deps/gsnap-chimera.Tpo -c -o gsnap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gsnap-chimera.Tpo .deps/gsnap-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3.o -MD -MP -MF .deps/gsnap-stage3.Tpo -c -o gsnap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gsnap-stage3.Tpo .deps/gsnap-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicestringpool.o -MD -MP -MF .deps/gsnap-splicestringpool.Tpo -c -o gsnap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/gsnap-splicestringpool.Tpo .deps/gsnap-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie_build.o -MD -MP -MF .deps/gsnap-splicetrie_build.Tpo -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
mv -f .deps/gsnap-splicetrie_build.Tpo .deps/gsnap-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie.o -MD -MP -MF .deps/gsnap-splicetrie.Tpo -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gsnap-splicetrie.Tpo .deps/gsnap-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splice.o -MD -MP -MF .deps/gsnap-splice.Tpo -c -o gsnap-splice.o `test -f 'splice.c' || echo './'`splice.c
mv -f .deps/gsnap-splice.Tpo .deps/gsnap-splice.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indel.o -MD -MP -MF .deps/gsnap-indel.Tpo -c -o gsnap-indel.o `test -f 'indel.c' || echo './'`indel.c
mv -f .deps/gsnap-indel.Tpo .deps/gsnap-indel.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-access.o -MD -MP -MF .deps/gsnap-bitpack64-access.Tpo -c -o gsnap-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/gsnap-bitpack64-access.Tpo .deps/gsnap-bitpack64-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sarray-read.o -MD -MP -MF .deps/gsnap-sarray-read.Tpo -c -o gsnap-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c
mv -f .deps/gsnap-sarray-read.Tpo .deps/gsnap-sarray-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage1hr.o -MD -MP -MF .deps/gsnap-stage1hr.Tpo -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
mv -f .deps/gsnap-stage1hr.Tpo .deps/gsnap-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-request.o -MD -MP -MF .deps/gsnap-request.Tpo -c -o gsnap-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gsnap-request.Tpo .deps/gsnap-request.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-resulthr.o -MD -MP -MF .deps/gsnap-resulthr.Tpo -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/gsnap-resulthr.Tpo .deps/gsnap-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-inbuffer.o -MD -MP -MF .deps/gsnap-inbuffer.Tpo -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gsnap-inbuffer.Tpo .deps/gsnap-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samheader.o -MD -MP -MF .deps/gsnap-samheader.Tpo -c -o gsnap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gsnap-samheader.Tpo .deps/gsnap-samheader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-outbuffer.o -MD -MP -MF .deps/gsnap-outbuffer.Tpo -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gsnap-outbuffer.Tpo .deps/gsnap-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-datadir.o -MD -MP -MF .deps/gsnap-datadir.Tpo -c -o gsnap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gsnap-datadir.Tpo .deps/gsnap-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt.o -MD -MP -MF .deps/gsnap-getopt.Tpo -c -o gsnap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gsnap-getopt.Tpo .deps/gsnap-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt1.o -MD -MP -MF .deps/gsnap-getopt1.Tpo -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gsnap-getopt1.Tpo .deps/gsnap-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gsnap.o -MD -MP -MF .deps/gsnap-gsnap.Tpo -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
mv -f .deps/gsnap-gsnap.Tpo .deps/gsnap-gsnap.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3     -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o  -lz -lbz2  -lm 
libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-except.o -MD -MP -MF .deps/gsnapl-except.Tpo -c -o gsnapl-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gsnapl-except.Tpo .deps/gsnapl-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-assert.o -MD -MP -MF .deps/gsnapl-assert.Tpo -c -o gsnapl-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gsnapl-assert.Tpo .deps/gsnapl-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mem.o -MD -MP -MF .deps/gsnapl-mem.Tpo -c -o gsnapl-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gsnapl-mem.Tpo .deps/gsnapl-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intlist.o -MD -MP -MF .deps/gsnapl-intlist.Tpo -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gsnapl-intlist.Tpo .deps/gsnapl-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-list.o -MD -MP -MF .deps/gsnapl-list.Tpo -c -o gsnapl-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gsnapl-list.Tpo .deps/gsnapl-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-littleendian.o -MD -MP -MF .deps/gsnapl-littleendian.Tpo -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/gsnapl-littleendian.Tpo .deps/gsnapl-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bigendian.o -MD -MP -MF .deps/gsnapl-bigendian.Tpo -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/gsnapl-bigendian.Tpo .deps/gsnapl-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-univinterval.o -MD -MP -MF .deps/gsnapl-univinterval.Tpo -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/gsnapl-univinterval.Tpo .deps/gsnapl-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-interval.o -MD -MP -MF .deps/gsnapl-interval.Tpo -c -o gsnapl-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gsnapl-interval.Tpo .deps/gsnapl-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uintlist.o -MD -MP -MF .deps/gsnapl-uintlist.Tpo -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gsnapl-uintlist.Tpo .deps/gsnapl-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uint8list.o -MD -MP -MF .deps/gsnapl-uint8list.Tpo -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
uint8list.c: In function ‘Uint8list_to_string’:
uint8list.c:202:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
       sprintf(Buffer,"%u,",Uint8list_head(p));
                      ^
uint8list.c:205:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",Uint8list_head(p));
                    ^
uint8list.c:211:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
       sprintf(Buffer,"%u,",Uint8list_head(p));
                      ^
uint8list.c:214:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",Uint8list_head(p));
                    ^
mv -f .deps/gsnapl-uint8list.Tpo .deps/gsnapl-uint8list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stopwatch.o -MD -MP -MF .deps/gsnapl-stopwatch.Tpo -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gsnapl-stopwatch.Tpo .deps/gsnapl-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-access.o -MD -MP -MF .deps/gsnapl-access.Tpo -c -o gsnapl-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/gsnapl-access.Tpo .deps/gsnapl-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read-univ.o -MD -MP -MF .deps/gsnapl-iit-read-univ.Tpo -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/gsnapl-iit-read-univ.Tpo .deps/gsnapl-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read.o -MD -MP -MF .deps/gsnapl-iit-read.Tpo -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/gsnapl-iit-read.Tpo .deps/gsnapl-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-md5.o -MD -MP -MF .deps/gsnapl-md5.Tpo -c -o gsnapl-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gsnapl-md5.Tpo .deps/gsnapl-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bzip2.o -MD -MP -MF .deps/gsnapl-bzip2.Tpo -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/gsnapl-bzip2.Tpo .deps/gsnapl-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sequence.o -MD -MP -MF .deps/gsnapl-sequence.Tpo -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gsnapl-sequence.Tpo .deps/gsnapl-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-reader.o -MD -MP -MF .deps/gsnapl-reader.Tpo -c -o gsnapl-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/gsnapl-reader.Tpo .deps/gsnapl-reader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genomicpos.o -MD -MP -MF .deps/gsnapl-genomicpos.Tpo -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gsnapl-genomicpos.Tpo .deps/gsnapl-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-compress.o -MD -MP -MF .deps/gsnapl-compress.Tpo -c -o gsnapl-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/gsnapl-compress.Tpo .deps/gsnapl-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome.o -MD -MP -MF .deps/gsnapl-genome.Tpo -c -o gsnapl-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/gsnapl-genome.Tpo .deps/gsnapl-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_hr.o -MD -MP -MF .deps/gsnapl-genome_hr.Tpo -c -o gsnapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/gsnapl-genome_hr.Tpo .deps/gsnapl-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_sites.o -MD -MP -MF .deps/gsnapl-genome_sites.Tpo -c -o gsnapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
genome_sites.c: In function ‘Genome_print_blocks’:
genome_sites.c:24729:10: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%u\t",startblock/3*32U);
          ^
genome_sites.c:24744:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%u\t",ptr/3*32U);
            ^
genome_sites.c:24751:10: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%u\t",(endblock+3)/3*32U);
          ^
mv -f .deps/gsnapl-genome_sites.Tpo .deps/gsnapl-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-read.o -MD -MP -MF .deps/gsnapl-bitpack64-read.Tpo -c -o gsnapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/gsnapl-bitpack64-read.Tpo .deps/gsnapl-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb.o -MD -MP -MF .deps/gsnapl-indexdb.Tpo -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gsnapl-indexdb.Tpo .deps/gsnapl-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb_hr.o -MD -MP -MF .deps/gsnapl-indexdb_hr.Tpo -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘Compoundpos_dump’:
indexdb_hr.c:1008:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm);
              ^
indexdb_hr.c: In function ‘heap_even_dump’:
indexdb_hr.c:1232:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("#%d--%d:%u  ",i,batch->nentries,batch->position);
            ^
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/gsnapl-indexdb_hr.Tpo .deps/gsnapl-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligo.o -MD -MP -MF .deps/gsnapl-oligo.Tpo -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/gsnapl-oligo.Tpo .deps/gsnapl-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrom.o -MD -MP -MF .deps/gsnapl-chrom.Tpo -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gsnapl-chrom.Tpo .deps/gsnapl-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-segmentpos.o -MD -MP -MF .deps/gsnapl-segmentpos.Tpo -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
segmentpos.c: In function ‘Segmentpos_print’:
segmentpos.c:90:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length);
              ^
mv -f .deps/gsnapl-segmentpos.Tpo .deps/gsnapl-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrnum.o -MD -MP -MF .deps/gsnapl-chrnum.Tpo -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/gsnapl-chrnum.Tpo .deps/gsnapl-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent_hr.o -MD -MP -MF .deps/gsnapl-maxent_hr.Tpo -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/gsnapl-maxent_hr.Tpo .deps/gsnapl-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samprint.o -MD -MP -MF .deps/gsnapl-samprint.Tpo -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo './'`samprint.c
mv -f .deps/gsnapl-samprint.Tpo .deps/gsnapl-samprint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mapq.o -MD -MP -MF .deps/gsnapl-mapq.Tpo -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/gsnapl-mapq.Tpo .deps/gsnapl-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-shortread.o -MD -MP -MF .deps/gsnapl-shortread.Tpo -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/gsnapl-shortread.Tpo .deps/gsnapl-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-substring.o -MD -MP -MF .deps/gsnapl-substring.Tpo -c -o gsnapl-substring.o `test -f 'substring.c' || echo './'`substring.c
substring.c: In function ‘Substring_print_ends’:
substring.c:1005:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend);
            ^
substring.c:1005:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
substring.c: In function ‘print_coordinates’:
substring.c:3536:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U,
                  ^
substring.c:3536:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
substring.c:3539:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset,
                  ^
substring.c:3539:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
substring.c:3544:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset,
                  ^
substring.c:3544:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
substring.c:3547:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U,
                  ^
substring.c:3547:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/gsnapl-substring.Tpo .deps/gsnapl-substring.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3hr.o -MD -MP -MF .deps/gsnapl-stage3hr.Tpo -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/gsnapl-stage3hr.Tpo .deps/gsnapl-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-goby.o -MD -MP -MF .deps/gsnapl-goby.Tpo -c -o gsnapl-goby.o `test -f 'goby.c' || echo './'`goby.c
mv -f .deps/gsnapl-goby.Tpo .deps/gsnapl-goby.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-spanningelt.o -MD -MP -MF .deps/gsnapl-spanningelt.Tpo -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/gsnapl-spanningelt.Tpo .deps/gsnapl-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cmet.o -MD -MP -MF .deps/gsnapl-cmet.Tpo -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/gsnapl-cmet.Tpo .deps/gsnapl-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-atoi.o -MD -MP -MF .deps/gsnapl-atoi.Tpo -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/gsnapl-atoi.Tpo .deps/gsnapl-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent.o -MD -MP -MF .deps/gsnapl-maxent.Tpo -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/gsnapl-maxent.Tpo .deps/gsnapl-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pair.o -MD -MP -MF .deps/gsnapl-pair.Tpo -c -o gsnapl-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c: In function ‘print_genomic_sequence’:
pair.c:546:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘print_genomicalt_sequence’:
pair.c:573:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘compute_margin’:
pair.c:600:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP);
                    ^
pair.c:607:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘Pair_print_coordinates’:
pair.c:1272:13: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(fp,"%u %u %c",this->genomepos + ONEBASEDP,
             ^
pair.c:1276:13: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(fp,"%s:%u %u %c",chrstring,
             ^
pair.c: In function ‘Pair_print_exonsummary’:
pair.c:1790:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                 ^
pair.c:1790:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1799:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                 ^
pair.c:1799:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1913:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ^
pair.c:1913:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1922:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ^
pair.c:1922:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c: In function ‘Pair_print_compressed’:
pair.c:6986:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
              ^
pair.c:6986:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/gsnapl-pair.Tpo .deps/gsnapl-pair.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pairpool.o -MD -MP -MF .deps/gsnapl-pairpool.Tpo -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/gsnapl-pairpool.Tpo .deps/gsnapl-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diag.o -MD -MP -MF .deps/gsnapl-diag.Tpo -c -o gsnapl-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/gsnapl-diag.Tpo .deps/gsnapl-diag.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diagpool.o -MD -MP -MF .deps/gsnapl-diagpool.Tpo -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/gsnapl-diagpool.Tpo .deps/gsnapl-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-orderstat.o -MD -MP -MF .deps/gsnapl-orderstat.Tpo -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/gsnapl-orderstat.Tpo .deps/gsnapl-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligoindex_hr.o -MD -MP -MF .deps/gsnapl-oligoindex_hr.Tpo -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/gsnapl-oligoindex_hr.Tpo .deps/gsnapl-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cellpool.o -MD -MP -MF .deps/gsnapl-cellpool.Tpo -c -o gsnapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/gsnapl-cellpool.Tpo .deps/gsnapl-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage2.o -MD -MP -MF .deps/gsnapl-stage2.Tpo -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
mv -f .deps/gsnapl-stage2.Tpo .deps/gsnapl-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intron.o -MD -MP -MF .deps/gsnapl-intron.Tpo -c -o gsnapl-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/gsnapl-intron.Tpo .deps/gsnapl-intron.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-boyer-moore.o -MD -MP -MF .deps/gsnapl-boyer-moore.Tpo -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/gsnapl-boyer-moore.Tpo .deps/gsnapl-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-changepoint.o -MD -MP -MF .deps/gsnapl-changepoint.Tpo -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/gsnapl-changepoint.Tpo .deps/gsnapl-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pbinom.o -MD -MP -MF .deps/gsnapl-pbinom.Tpo -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/gsnapl-pbinom.Tpo .deps/gsnapl-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-dynprog.o -MD -MP -MF .deps/gsnapl-dynprog.Tpo -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/gsnapl-dynprog.Tpo .deps/gsnapl-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gbuffer.o -MD -MP -MF .deps/gsnapl-gbuffer.Tpo -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
mv -f .deps/gsnapl-gbuffer.Tpo .deps/gsnapl-gbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-translation.o -MD -MP -MF .deps/gsnapl-translation.Tpo -c -o gsnapl-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/gsnapl-translation.Tpo .deps/gsnapl-translation.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-doublelist.o -MD -MP -MF .deps/gsnapl-doublelist.Tpo -c -o gsnapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/gsnapl-doublelist.Tpo .deps/gsnapl-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-smooth.o -MD -MP -MF .deps/gsnapl-smooth.Tpo -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/gsnapl-smooth.Tpo .deps/gsnapl-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chimera.o -MD -MP -MF .deps/gsnapl-chimera.Tpo -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/gsnapl-chimera.Tpo .deps/gsnapl-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3.o -MD -MP -MF .deps/gsnapl-stage3.Tpo -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/gsnapl-stage3.Tpo .deps/gsnapl-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicestringpool.o -MD -MP -MF .deps/gsnapl-splicestringpool.Tpo -c -o gsnapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/gsnapl-splicestringpool.Tpo .deps/gsnapl-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie_build.o -MD -MP -MF .deps/gsnapl-splicetrie_build.Tpo -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
splicetrie_build.c: In function ‘Splicetrie_dump’:
splicetrie_build.c:132:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%d %u",(int) leaf,position);
            ^
splicetrie_build.c:146:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%d %u",(int) leaf,position);
              ^
mv -f .deps/gsnapl-splicetrie_build.Tpo .deps/gsnapl-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie.o -MD -MP -MF .deps/gsnapl-splicetrie.Tpo -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/gsnapl-splicetrie.Tpo .deps/gsnapl-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splice.o -MD -MP -MF .deps/gsnapl-splice.Tpo -c -o gsnapl-splice.o `test -f 'splice.c' || echo './'`splice.c
mv -f .deps/gsnapl-splice.Tpo .deps/gsnapl-splice.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indel.o -MD -MP -MF .deps/gsnapl-indel.Tpo -c -o gsnapl-indel.o `test -f 'indel.c' || echo './'`indel.c
mv -f .deps/gsnapl-indel.Tpo .deps/gsnapl-indel.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-access.o -MD -MP -MF .deps/gsnapl-bitpack64-access.Tpo -c -o gsnapl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/gsnapl-bitpack64-access.Tpo .deps/gsnapl-bitpack64-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sarray-read.o -MD -MP -MF .deps/gsnapl-sarray-read.Tpo -c -o gsnapl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c
sarray-read.c: In function ‘Sarray_new’:
sarray-read.c:302:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T));
               ^
sarray-read.c:368:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2,
               ^
sarray-read.c:434:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T),
               ^
sarray-read.c:526:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T));
               ^
sarray-read.c:653:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,
               ^
sarray-read.c: In function ‘Elt_dump_list’:
sarray-read.c:1667:9: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%d..%d:%u\t",elt->querystart,elt->queryend,elt->positions[k]);
         ^
sarray-read.c: In function ‘Elt_dump’:
sarray-read.c:1682:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%d..%d:%u\n",elt->querystart,elt->queryend,elt->positions[k]);
            ^
sarray-read.c: In function ‘collect_elt_matches’:
sarray-read.c:2170:11: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
     array = Uintlist_to_array(&n,difflist);
           ^
sarray-read.c:2442:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:2442:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
             ^
sarray-read.c:2456:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          /*ambcoords_donor*/NULL,ambcoords,
                                  ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:2499:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:2499:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
             ^
sarray-read.c:2513:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          ambcoords,/*ambcoords_acceptor*/NULL,
          ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:2643:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:2643:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
             ^
sarray-read.c:2656:36: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
            /*ambcoords_donor*/NULL,ambcoords,
                                    ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:2699:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:2699:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
             ^
sarray-read.c:2712:12: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
            ambcoords,/*ambcoords_acceptor*/NULL,
            ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:2752:11: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
     array = Uintlist_to_array(&n,difflist);
           ^
sarray-read.c:3024:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:3024:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
             ^
sarray-read.c:3038:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          /*ambcoords_donor*/NULL,ambcoords,
                                  ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:3082:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:3082:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
             ^
sarray-read.c:3096:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          ambcoords,/*ambcoords_acceptor*/NULL,
          ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:3217:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:3217:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
             ^
sarray-read.c:3231:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          /*ambcoords_donor*/NULL,ambcoords,
                                  ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:3274:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:3274:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
             ^
sarray-read.c:3288:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          ambcoords,/*ambcoords_acceptor*/NULL,
          ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
mv -f .deps/gsnapl-sarray-read.Tpo .deps/gsnapl-sarray-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage1hr.o -MD -MP -MF .deps/gsnapl-stage1hr.Tpo -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
stage1hr.c: In function ‘find_singlesplices_plus’:
stage1hr.c:6629:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n",
                     ^
stage1hr.c:6629:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6629:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n",
                     ^
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 6 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 7 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 9 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c: In function ‘find_singlesplices_minus’:
stage1hr.c:7145:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n",
                     ^
stage1hr.c:7145:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:7145:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:7284:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n",
                     ^
stage1hr.c:7284:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:7284:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/gsnapl-stage1hr.Tpo .deps/gsnapl-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-request.o -MD -MP -MF .deps/gsnapl-request.Tpo -c -o gsnapl-request.o `test -f 'request.c' || echo './'`request.c
mv -f .deps/gsnapl-request.Tpo .deps/gsnapl-request.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-resulthr.o -MD -MP -MF .deps/gsnapl-resulthr.Tpo -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/gsnapl-resulthr.Tpo .deps/gsnapl-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-inbuffer.o -MD -MP -MF .deps/gsnapl-inbuffer.Tpo -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
mv -f .deps/gsnapl-inbuffer.Tpo .deps/gsnapl-inbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samheader.o -MD -MP -MF .deps/gsnapl-samheader.Tpo -c -o gsnapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
mv -f .deps/gsnapl-samheader.Tpo .deps/gsnapl-samheader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-outbuffer.o -MD -MP -MF .deps/gsnapl-outbuffer.Tpo -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
mv -f .deps/gsnapl-outbuffer.Tpo .deps/gsnapl-outbuffer.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-datadir.o -MD -MP -MF .deps/gsnapl-datadir.Tpo -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gsnapl-datadir.Tpo .deps/gsnapl-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt.o -MD -MP -MF .deps/gsnapl-getopt.Tpo -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gsnapl-getopt.Tpo .deps/gsnapl-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt1.o -MD -MP -MF .deps/gsnapl-getopt1.Tpo -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gsnapl-getopt1.Tpo .deps/gsnapl-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gsnap.o -MD -MP -MF .deps/gsnapl-gsnap.Tpo -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c
mv -f .deps/gsnapl-gsnap.Tpo .deps/gsnapl-gsnap.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx   -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3     -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o  -lz -lbz2  -lm 
libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-except.o -MD -MP -MF .deps/uniqscan-except.Tpo -c -o uniqscan-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/uniqscan-except.Tpo .deps/uniqscan-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-assert.o -MD -MP -MF .deps/uniqscan-assert.Tpo -c -o uniqscan-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/uniqscan-assert.Tpo .deps/uniqscan-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mem.o -MD -MP -MF .deps/uniqscan-mem.Tpo -c -o uniqscan-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/uniqscan-mem.Tpo .deps/uniqscan-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intlist.o -MD -MP -MF .deps/uniqscan-intlist.Tpo -c -o uniqscan-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/uniqscan-intlist.Tpo .deps/uniqscan-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-list.o -MD -MP -MF .deps/uniqscan-list.Tpo -c -o uniqscan-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/uniqscan-list.Tpo .deps/uniqscan-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-littleendian.o -MD -MP -MF .deps/uniqscan-littleendian.Tpo -c -o uniqscan-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/uniqscan-littleendian.Tpo .deps/uniqscan-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bigendian.o -MD -MP -MF .deps/uniqscan-bigendian.Tpo -c -o uniqscan-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/uniqscan-bigendian.Tpo .deps/uniqscan-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-univinterval.o -MD -MP -MF .deps/uniqscan-univinterval.Tpo -c -o uniqscan-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
mv -f .deps/uniqscan-univinterval.Tpo .deps/uniqscan-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-interval.o -MD -MP -MF .deps/uniqscan-interval.Tpo -c -o uniqscan-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/uniqscan-interval.Tpo .deps/uniqscan-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uintlist.o -MD -MP -MF .deps/uniqscan-uintlist.Tpo -c -o uniqscan-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/uniqscan-uintlist.Tpo .deps/uniqscan-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stopwatch.o -MD -MP -MF .deps/uniqscan-stopwatch.Tpo -c -o uniqscan-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/uniqscan-stopwatch.Tpo .deps/uniqscan-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-access.o -MD -MP -MF .deps/uniqscan-access.Tpo -c -o uniqscan-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/uniqscan-access.Tpo .deps/uniqscan-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read-univ.o -MD -MP -MF .deps/uniqscan-iit-read-univ.Tpo -c -o uniqscan-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/uniqscan-iit-read-univ.Tpo .deps/uniqscan-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read.o -MD -MP -MF .deps/uniqscan-iit-read.Tpo -c -o uniqscan-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/uniqscan-iit-read.Tpo .deps/uniqscan-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-md5.o -MD -MP -MF .deps/uniqscan-md5.Tpo -c -o uniqscan-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/uniqscan-md5.Tpo .deps/uniqscan-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bzip2.o -MD -MP -MF .deps/uniqscan-bzip2.Tpo -c -o uniqscan-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/uniqscan-bzip2.Tpo .deps/uniqscan-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sequence.o -MD -MP -MF .deps/uniqscan-sequence.Tpo -c -o uniqscan-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/uniqscan-sequence.Tpo .deps/uniqscan-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-reader.o -MD -MP -MF .deps/uniqscan-reader.Tpo -c -o uniqscan-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/uniqscan-reader.Tpo .deps/uniqscan-reader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genomicpos.o -MD -MP -MF .deps/uniqscan-genomicpos.Tpo -c -o uniqscan-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/uniqscan-genomicpos.Tpo .deps/uniqscan-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-compress.o -MD -MP -MF .deps/uniqscan-compress.Tpo -c -o uniqscan-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/uniqscan-compress.Tpo .deps/uniqscan-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome.o -MD -MP -MF .deps/uniqscan-genome.Tpo -c -o uniqscan-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/uniqscan-genome.Tpo .deps/uniqscan-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_hr.o -MD -MP -MF .deps/uniqscan-genome_hr.Tpo -c -o uniqscan-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/uniqscan-genome_hr.Tpo .deps/uniqscan-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_sites.o -MD -MP -MF .deps/uniqscan-genome_sites.Tpo -c -o uniqscan-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
mv -f .deps/uniqscan-genome_sites.Tpo .deps/uniqscan-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-read.o -MD -MP -MF .deps/uniqscan-bitpack64-read.Tpo -c -o uniqscan-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/uniqscan-bitpack64-read.Tpo .deps/uniqscan-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb.o -MD -MP -MF .deps/uniqscan-indexdb.Tpo -c -o uniqscan-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/uniqscan-indexdb.Tpo .deps/uniqscan-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb_hr.o -MD -MP -MF .deps/uniqscan-indexdb_hr.Tpo -c -o uniqscan-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/uniqscan-indexdb_hr.Tpo .deps/uniqscan-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligo.o -MD -MP -MF .deps/uniqscan-oligo.Tpo -c -o uniqscan-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/uniqscan-oligo.Tpo .deps/uniqscan-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrom.o -MD -MP -MF .deps/uniqscan-chrom.Tpo -c -o uniqscan-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/uniqscan-chrom.Tpo .deps/uniqscan-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-segmentpos.o -MD -MP -MF .deps/uniqscan-segmentpos.Tpo -c -o uniqscan-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/uniqscan-segmentpos.Tpo .deps/uniqscan-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrnum.o -MD -MP -MF .deps/uniqscan-chrnum.Tpo -c -o uniqscan-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/uniqscan-chrnum.Tpo .deps/uniqscan-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent_hr.o -MD -MP -MF .deps/uniqscan-maxent_hr.Tpo -c -o uniqscan-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/uniqscan-maxent_hr.Tpo .deps/uniqscan-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mapq.o -MD -MP -MF .deps/uniqscan-mapq.Tpo -c -o uniqscan-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/uniqscan-mapq.Tpo .deps/uniqscan-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-shortread.o -MD -MP -MF .deps/uniqscan-shortread.Tpo -c -o uniqscan-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/uniqscan-shortread.Tpo .deps/uniqscan-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-substring.o -MD -MP -MF .deps/uniqscan-substring.Tpo -c -o uniqscan-substring.o `test -f 'substring.c' || echo './'`substring.c
mv -f .deps/uniqscan-substring.Tpo .deps/uniqscan-substring.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3hr.o -MD -MP -MF .deps/uniqscan-stage3hr.Tpo -c -o uniqscan-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/uniqscan-stage3hr.Tpo .deps/uniqscan-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-spanningelt.o -MD -MP -MF .deps/uniqscan-spanningelt.Tpo -c -o uniqscan-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/uniqscan-spanningelt.Tpo .deps/uniqscan-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cmet.o -MD -MP -MF .deps/uniqscan-cmet.Tpo -c -o uniqscan-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/uniqscan-cmet.Tpo .deps/uniqscan-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-atoi.o -MD -MP -MF .deps/uniqscan-atoi.Tpo -c -o uniqscan-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/uniqscan-atoi.Tpo .deps/uniqscan-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent.o -MD -MP -MF .deps/uniqscan-maxent.Tpo -c -o uniqscan-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/uniqscan-maxent.Tpo .deps/uniqscan-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pair.o -MD -MP -MF .deps/uniqscan-pair.Tpo -c -o uniqscan-pair.o `test -f 'pair.c' || echo './'`pair.c
mv -f .deps/uniqscan-pair.Tpo .deps/uniqscan-pair.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pairpool.o -MD -MP -MF .deps/uniqscan-pairpool.Tpo -c -o uniqscan-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/uniqscan-pairpool.Tpo .deps/uniqscan-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diag.o -MD -MP -MF .deps/uniqscan-diag.Tpo -c -o uniqscan-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/uniqscan-diag.Tpo .deps/uniqscan-diag.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diagpool.o -MD -MP -MF .deps/uniqscan-diagpool.Tpo -c -o uniqscan-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/uniqscan-diagpool.Tpo .deps/uniqscan-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-orderstat.o -MD -MP -MF .deps/uniqscan-orderstat.Tpo -c -o uniqscan-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/uniqscan-orderstat.Tpo .deps/uniqscan-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligoindex_hr.o -MD -MP -MF .deps/uniqscan-oligoindex_hr.Tpo -c -o uniqscan-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/uniqscan-oligoindex_hr.Tpo .deps/uniqscan-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cellpool.o -MD -MP -MF .deps/uniqscan-cellpool.Tpo -c -o uniqscan-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/uniqscan-cellpool.Tpo .deps/uniqscan-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage2.o -MD -MP -MF .deps/uniqscan-stage2.Tpo -c -o uniqscan-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
mv -f .deps/uniqscan-stage2.Tpo .deps/uniqscan-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intron.o -MD -MP -MF .deps/uniqscan-intron.Tpo -c -o uniqscan-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/uniqscan-intron.Tpo .deps/uniqscan-intron.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-boyer-moore.o -MD -MP -MF .deps/uniqscan-boyer-moore.Tpo -c -o uniqscan-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/uniqscan-boyer-moore.Tpo .deps/uniqscan-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-changepoint.o -MD -MP -MF .deps/uniqscan-changepoint.Tpo -c -o uniqscan-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/uniqscan-changepoint.Tpo .deps/uniqscan-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pbinom.o -MD -MP -MF .deps/uniqscan-pbinom.Tpo -c -o uniqscan-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/uniqscan-pbinom.Tpo .deps/uniqscan-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-dynprog.o -MD -MP -MF .deps/uniqscan-dynprog.Tpo -c -o uniqscan-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/uniqscan-dynprog.Tpo .deps/uniqscan-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-translation.o -MD -MP -MF .deps/uniqscan-translation.Tpo -c -o uniqscan-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/uniqscan-translation.Tpo .deps/uniqscan-translation.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-doublelist.o -MD -MP -MF .deps/uniqscan-doublelist.Tpo -c -o uniqscan-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/uniqscan-doublelist.Tpo .deps/uniqscan-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-smooth.o -MD -MP -MF .deps/uniqscan-smooth.Tpo -c -o uniqscan-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/uniqscan-smooth.Tpo .deps/uniqscan-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chimera.o -MD -MP -MF .deps/uniqscan-chimera.Tpo -c -o uniqscan-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/uniqscan-chimera.Tpo .deps/uniqscan-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3.o -MD -MP -MF .deps/uniqscan-stage3.Tpo -c -o uniqscan-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/uniqscan-stage3.Tpo .deps/uniqscan-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicestringpool.o -MD -MP -MF .deps/uniqscan-splicestringpool.Tpo -c -o uniqscan-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/uniqscan-splicestringpool.Tpo .deps/uniqscan-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie_build.o -MD -MP -MF .deps/uniqscan-splicetrie_build.Tpo -c -o uniqscan-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
mv -f .deps/uniqscan-splicetrie_build.Tpo .deps/uniqscan-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie.o -MD -MP -MF .deps/uniqscan-splicetrie.Tpo -c -o uniqscan-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/uniqscan-splicetrie.Tpo .deps/uniqscan-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splice.o -MD -MP -MF .deps/uniqscan-splice.Tpo -c -o uniqscan-splice.o `test -f 'splice.c' || echo './'`splice.c
mv -f .deps/uniqscan-splice.Tpo .deps/uniqscan-splice.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indel.o -MD -MP -MF .deps/uniqscan-indel.Tpo -c -o uniqscan-indel.o `test -f 'indel.c' || echo './'`indel.c
mv -f .deps/uniqscan-indel.Tpo .deps/uniqscan-indel.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-access.o -MD -MP -MF .deps/uniqscan-bitpack64-access.Tpo -c -o uniqscan-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/uniqscan-bitpack64-access.Tpo .deps/uniqscan-bitpack64-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sarray-read.o -MD -MP -MF .deps/uniqscan-sarray-read.Tpo -c -o uniqscan-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c
mv -f .deps/uniqscan-sarray-read.Tpo .deps/uniqscan-sarray-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage1hr.o -MD -MP -MF .deps/uniqscan-stage1hr.Tpo -c -o uniqscan-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
mv -f .deps/uniqscan-stage1hr.Tpo .deps/uniqscan-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-resulthr.o -MD -MP -MF .deps/uniqscan-resulthr.Tpo -c -o uniqscan-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/uniqscan-resulthr.Tpo .deps/uniqscan-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-datadir.o -MD -MP -MF .deps/uniqscan-datadir.Tpo -c -o uniqscan-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/uniqscan-datadir.Tpo .deps/uniqscan-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt.o -MD -MP -MF .deps/uniqscan-getopt.Tpo -c -o uniqscan-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/uniqscan-getopt.Tpo .deps/uniqscan-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt1.o -MD -MP -MF .deps/uniqscan-getopt1.Tpo -c -o uniqscan-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/uniqscan-getopt1.Tpo .deps/uniqscan-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uniqscan.o -MD -MP -MF .deps/uniqscan-uniqscan.Tpo -c -o uniqscan-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c
mv -f .deps/uniqscan-uniqscan.Tpo .deps/uniqscan-uniqscan.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3    -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o  -lz -lbz2 -lm 
libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-except.o -MD -MP -MF .deps/uniqscanl-except.Tpo -c -o uniqscanl-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/uniqscanl-except.Tpo .deps/uniqscanl-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-assert.o -MD -MP -MF .deps/uniqscanl-assert.Tpo -c -o uniqscanl-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/uniqscanl-assert.Tpo .deps/uniqscanl-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mem.o -MD -MP -MF .deps/uniqscanl-mem.Tpo -c -o uniqscanl-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/uniqscanl-mem.Tpo .deps/uniqscanl-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intlist.o -MD -MP -MF .deps/uniqscanl-intlist.Tpo -c -o uniqscanl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/uniqscanl-intlist.Tpo .deps/uniqscanl-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-list.o -MD -MP -MF .deps/uniqscanl-list.Tpo -c -o uniqscanl-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/uniqscanl-list.Tpo .deps/uniqscanl-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-littleendian.o -MD -MP -MF .deps/uniqscanl-littleendian.Tpo -c -o uniqscanl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/uniqscanl-littleendian.Tpo .deps/uniqscanl-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bigendian.o -MD -MP -MF .deps/uniqscanl-bigendian.Tpo -c -o uniqscanl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/uniqscanl-bigendian.Tpo .deps/uniqscanl-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-univinterval.o -MD -MP -MF .deps/uniqscanl-univinterval.Tpo -c -o uniqscanl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/uniqscanl-univinterval.Tpo .deps/uniqscanl-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-interval.o -MD -MP -MF .deps/uniqscanl-interval.Tpo -c -o uniqscanl-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/uniqscanl-interval.Tpo .deps/uniqscanl-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uintlist.o -MD -MP -MF .deps/uniqscanl-uintlist.Tpo -c -o uniqscanl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/uniqscanl-uintlist.Tpo .deps/uniqscanl-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uint8list.o -MD -MP -MF .deps/uniqscanl-uint8list.Tpo -c -o uniqscanl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c
uint8list.c: In function ‘Uint8list_to_string’:
uint8list.c:202:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
       sprintf(Buffer,"%u,",Uint8list_head(p));
                      ^
uint8list.c:205:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",Uint8list_head(p));
                    ^
uint8list.c:211:22: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
       sprintf(Buffer,"%u,",Uint8list_head(p));
                      ^
uint8list.c:214:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",Uint8list_head(p));
                    ^
mv -f .deps/uniqscanl-uint8list.Tpo .deps/uniqscanl-uint8list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stopwatch.o -MD -MP -MF .deps/uniqscanl-stopwatch.Tpo -c -o uniqscanl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/uniqscanl-stopwatch.Tpo .deps/uniqscanl-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-access.o -MD -MP -MF .deps/uniqscanl-access.Tpo -c -o uniqscanl-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/uniqscanl-access.Tpo .deps/uniqscanl-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read-univ.o -MD -MP -MF .deps/uniqscanl-iit-read-univ.Tpo -c -o uniqscanl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/uniqscanl-iit-read-univ.Tpo .deps/uniqscanl-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read.o -MD -MP -MF .deps/uniqscanl-iit-read.Tpo -c -o uniqscanl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/uniqscanl-iit-read.Tpo .deps/uniqscanl-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-md5.o -MD -MP -MF .deps/uniqscanl-md5.Tpo -c -o uniqscanl-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/uniqscanl-md5.Tpo .deps/uniqscanl-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bzip2.o -MD -MP -MF .deps/uniqscanl-bzip2.Tpo -c -o uniqscanl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/uniqscanl-bzip2.Tpo .deps/uniqscanl-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sequence.o -MD -MP -MF .deps/uniqscanl-sequence.Tpo -c -o uniqscanl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/uniqscanl-sequence.Tpo .deps/uniqscanl-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-reader.o -MD -MP -MF .deps/uniqscanl-reader.Tpo -c -o uniqscanl-reader.o `test -f 'reader.c' || echo './'`reader.c
mv -f .deps/uniqscanl-reader.Tpo .deps/uniqscanl-reader.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genomicpos.o -MD -MP -MF .deps/uniqscanl-genomicpos.Tpo -c -o uniqscanl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/uniqscanl-genomicpos.Tpo .deps/uniqscanl-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-compress.o -MD -MP -MF .deps/uniqscanl-compress.Tpo -c -o uniqscanl-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/uniqscanl-compress.Tpo .deps/uniqscanl-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome.o -MD -MP -MF .deps/uniqscanl-genome.Tpo -c -o uniqscanl-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/uniqscanl-genome.Tpo .deps/uniqscanl-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_hr.o -MD -MP -MF .deps/uniqscanl-genome_hr.Tpo -c -o uniqscanl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/uniqscanl-genome_hr.Tpo .deps/uniqscanl-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_sites.o -MD -MP -MF .deps/uniqscanl-genome_sites.Tpo -c -o uniqscanl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
genome_sites.c: In function ‘Genome_print_blocks’:
genome_sites.c:24729:10: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%u\t",startblock/3*32U);
          ^
genome_sites.c:24744:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%u\t",ptr/3*32U);
            ^
genome_sites.c:24751:10: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%u\t",(endblock+3)/3*32U);
          ^
mv -f .deps/uniqscanl-genome_sites.Tpo .deps/uniqscanl-genome_sites.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-read.o -MD -MP -MF .deps/uniqscanl-bitpack64-read.Tpo -c -o uniqscanl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/uniqscanl-bitpack64-read.Tpo .deps/uniqscanl-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb.o -MD -MP -MF .deps/uniqscanl-indexdb.Tpo -c -o uniqscanl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/uniqscanl-indexdb.Tpo .deps/uniqscanl-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb_hr.o -MD -MP -MF .deps/uniqscanl-indexdb_hr.Tpo -c -o uniqscanl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘Compoundpos_dump’:
indexdb_hr.c:1008:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf(" compound%d.%d:%u+%d\n",i,j,compoundpos->positions[i][j],diagterm);
              ^
indexdb_hr.c: In function ‘heap_even_dump’:
indexdb_hr.c:1232:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("#%d--%d:%u  ",i,batch->nentries,batch->position);
            ^
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:593:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/uniqscanl-indexdb_hr.Tpo .deps/uniqscanl-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligo.o -MD -MP -MF .deps/uniqscanl-oligo.Tpo -c -o uniqscanl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
mv -f .deps/uniqscanl-oligo.Tpo .deps/uniqscanl-oligo.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrom.o -MD -MP -MF .deps/uniqscanl-chrom.Tpo -c -o uniqscanl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/uniqscanl-chrom.Tpo .deps/uniqscanl-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-segmentpos.o -MD -MP -MF .deps/uniqscanl-segmentpos.Tpo -c -o uniqscanl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
segmentpos.c: In function ‘Segmentpos_print’:
segmentpos.c:90:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(fp,"%s\t%u\t%s\t%u\t%u\n",acc,chroffset+this->chrpos1,Chrom_string(this->chrom),this->chrpos1,this->length);
              ^
mv -f .deps/uniqscanl-segmentpos.Tpo .deps/uniqscanl-segmentpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrnum.o -MD -MP -MF .deps/uniqscanl-chrnum.Tpo -c -o uniqscanl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
mv -f .deps/uniqscanl-chrnum.Tpo .deps/uniqscanl-chrnum.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent_hr.o -MD -MP -MF .deps/uniqscanl-maxent_hr.Tpo -c -o uniqscanl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
mv -f .deps/uniqscanl-maxent_hr.Tpo .deps/uniqscanl-maxent_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mapq.o -MD -MP -MF .deps/uniqscanl-mapq.Tpo -c -o uniqscanl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c
mv -f .deps/uniqscanl-mapq.Tpo .deps/uniqscanl-mapq.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-shortread.o -MD -MP -MF .deps/uniqscanl-shortread.Tpo -c -o uniqscanl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c
mv -f .deps/uniqscanl-shortread.Tpo .deps/uniqscanl-shortread.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-substring.o -MD -MP -MF .deps/uniqscanl-substring.Tpo -c -o uniqscanl-substring.o `test -f 'substring.c' || echo './'`substring.c
substring.c: In function ‘Substring_print_ends’:
substring.c:1005:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("#%d:%u..%u ",chrnum,this->alignstart,this->alignend);
            ^
substring.c:1005:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
substring.c: In function ‘print_coordinates’:
substring.c:3536:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"+%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset + 1U,
                  ^
substring.c:3536:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
substring.c:3539:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"-%s:%u..%u",chr,substring->alignend_trim - substring->chroffset,
                  ^
substring.c:3539:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
substring.c:3544:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"-%s:%u..%u",chr,substring->alignstart_trim - substring->chroffset,
                  ^
substring.c:3544:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
substring.c:3547:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"+%s:%u..%u",chr,substring->alignend_trim - substring->chroffset + 1U,
                  ^
substring.c:3547:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/uniqscanl-substring.Tpo .deps/uniqscanl-substring.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3hr.o -MD -MP -MF .deps/uniqscanl-stage3hr.Tpo -c -o uniqscanl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c
mv -f .deps/uniqscanl-stage3hr.Tpo .deps/uniqscanl-stage3hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-spanningelt.o -MD -MP -MF .deps/uniqscanl-spanningelt.Tpo -c -o uniqscanl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c
mv -f .deps/uniqscanl-spanningelt.Tpo .deps/uniqscanl-spanningelt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cmet.o -MD -MP -MF .deps/uniqscanl-cmet.Tpo -c -o uniqscanl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/uniqscanl-cmet.Tpo .deps/uniqscanl-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-atoi.o -MD -MP -MF .deps/uniqscanl-atoi.Tpo -c -o uniqscanl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/uniqscanl-atoi.Tpo .deps/uniqscanl-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent.o -MD -MP -MF .deps/uniqscanl-maxent.Tpo -c -o uniqscanl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
mv -f .deps/uniqscanl-maxent.Tpo .deps/uniqscanl-maxent.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pair.o -MD -MP -MF .deps/uniqscanl-pair.Tpo -c -o uniqscanl-pair.o `test -f 'pair.c' || echo './'`pair.c
pair.c: In function ‘print_genomic_sequence’:
pair.c:546:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘print_genomicalt_sequence’:
pair.c:573:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘compute_margin’:
pair.c:600:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP);
                    ^
pair.c:607:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP);
                    ^
pair.c: In function ‘Pair_print_coordinates’:
pair.c:1272:13: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(fp,"%u %u %c",this->genomepos + ONEBASEDP,
             ^
pair.c:1276:13: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(fp,"%s:%u %u %c",chrstring,
             ^
pair.c: In function ‘Pair_print_exonsummary’:
pair.c:1790:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                 ^
pair.c:1790:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1799:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                 ^
pair.c:1799:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1913:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"%u-%u",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ^
pair.c:1913:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c:1922:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(fp,"(%u-%u)",chroffset+exon_genomestart,chroffset+exon_genomeend);
                  ^
pair.c:1922:18: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
pair.c: In function ‘Pair_print_compressed’:
pair.c:6986:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(fp," %u%s%u",position1 + ONEBASEDP,"..",position2 + ONEBASEDP);
              ^
pair.c:6986:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/uniqscanl-pair.Tpo .deps/uniqscanl-pair.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pairpool.o -MD -MP -MF .deps/uniqscanl-pairpool.Tpo -c -o uniqscanl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
mv -f .deps/uniqscanl-pairpool.Tpo .deps/uniqscanl-pairpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diag.o -MD -MP -MF .deps/uniqscanl-diag.Tpo -c -o uniqscanl-diag.o `test -f 'diag.c' || echo './'`diag.c
mv -f .deps/uniqscanl-diag.Tpo .deps/uniqscanl-diag.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diagpool.o -MD -MP -MF .deps/uniqscanl-diagpool.Tpo -c -o uniqscanl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
mv -f .deps/uniqscanl-diagpool.Tpo .deps/uniqscanl-diagpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-orderstat.o -MD -MP -MF .deps/uniqscanl-orderstat.Tpo -c -o uniqscanl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
mv -f .deps/uniqscanl-orderstat.Tpo .deps/uniqscanl-orderstat.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligoindex_hr.o -MD -MP -MF .deps/uniqscanl-oligoindex_hr.Tpo -c -o uniqscanl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
mv -f .deps/uniqscanl-oligoindex_hr.Tpo .deps/uniqscanl-oligoindex_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cellpool.o -MD -MP -MF .deps/uniqscanl-cellpool.Tpo -c -o uniqscanl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
mv -f .deps/uniqscanl-cellpool.Tpo .deps/uniqscanl-cellpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage2.o -MD -MP -MF .deps/uniqscanl-stage2.Tpo -c -o uniqscanl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
mv -f .deps/uniqscanl-stage2.Tpo .deps/uniqscanl-stage2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intron.o -MD -MP -MF .deps/uniqscanl-intron.Tpo -c -o uniqscanl-intron.o `test -f 'intron.c' || echo './'`intron.c
mv -f .deps/uniqscanl-intron.Tpo .deps/uniqscanl-intron.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-boyer-moore.o -MD -MP -MF .deps/uniqscanl-boyer-moore.Tpo -c -o uniqscanl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
mv -f .deps/uniqscanl-boyer-moore.Tpo .deps/uniqscanl-boyer-moore.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-changepoint.o -MD -MP -MF .deps/uniqscanl-changepoint.Tpo -c -o uniqscanl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
mv -f .deps/uniqscanl-changepoint.Tpo .deps/uniqscanl-changepoint.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pbinom.o -MD -MP -MF .deps/uniqscanl-pbinom.Tpo -c -o uniqscanl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
mv -f .deps/uniqscanl-pbinom.Tpo .deps/uniqscanl-pbinom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-dynprog.o -MD -MP -MF .deps/uniqscanl-dynprog.Tpo -c -o uniqscanl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
mv -f .deps/uniqscanl-dynprog.Tpo .deps/uniqscanl-dynprog.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-translation.o -MD -MP -MF .deps/uniqscanl-translation.Tpo -c -o uniqscanl-translation.o `test -f 'translation.c' || echo './'`translation.c
mv -f .deps/uniqscanl-translation.Tpo .deps/uniqscanl-translation.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-doublelist.o -MD -MP -MF .deps/uniqscanl-doublelist.Tpo -c -o uniqscanl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
mv -f .deps/uniqscanl-doublelist.Tpo .deps/uniqscanl-doublelist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-smooth.o -MD -MP -MF .deps/uniqscanl-smooth.Tpo -c -o uniqscanl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
mv -f .deps/uniqscanl-smooth.Tpo .deps/uniqscanl-smooth.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chimera.o -MD -MP -MF .deps/uniqscanl-chimera.Tpo -c -o uniqscanl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
mv -f .deps/uniqscanl-chimera.Tpo .deps/uniqscanl-chimera.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3.o -MD -MP -MF .deps/uniqscanl-stage3.Tpo -c -o uniqscanl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
mv -f .deps/uniqscanl-stage3.Tpo .deps/uniqscanl-stage3.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicestringpool.o -MD -MP -MF .deps/uniqscanl-splicestringpool.Tpo -c -o uniqscanl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
mv -f .deps/uniqscanl-splicestringpool.Tpo .deps/uniqscanl-splicestringpool.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie_build.o -MD -MP -MF .deps/uniqscanl-splicetrie_build.Tpo -c -o uniqscanl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
splicetrie_build.c: In function ‘Splicetrie_dump’:
splicetrie_build.c:132:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%d %u",(int) leaf,position);
            ^
splicetrie_build.c:146:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%d %u",(int) leaf,position);
              ^
mv -f .deps/uniqscanl-splicetrie_build.Tpo .deps/uniqscanl-splicetrie_build.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie.o -MD -MP -MF .deps/uniqscanl-splicetrie.Tpo -c -o uniqscanl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
mv -f .deps/uniqscanl-splicetrie.Tpo .deps/uniqscanl-splicetrie.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splice.o -MD -MP -MF .deps/uniqscanl-splice.Tpo -c -o uniqscanl-splice.o `test -f 'splice.c' || echo './'`splice.c
mv -f .deps/uniqscanl-splice.Tpo .deps/uniqscanl-splice.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indel.o -MD -MP -MF .deps/uniqscanl-indel.Tpo -c -o uniqscanl-indel.o `test -f 'indel.c' || echo './'`indel.c
mv -f .deps/uniqscanl-indel.Tpo .deps/uniqscanl-indel.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-access.o -MD -MP -MF .deps/uniqscanl-bitpack64-access.Tpo -c -o uniqscanl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c
mv -f .deps/uniqscanl-bitpack64-access.Tpo .deps/uniqscanl-bitpack64-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sarray-read.o -MD -MP -MF .deps/uniqscanl-sarray-read.Tpo -c -o uniqscanl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c
sarray-read.c: In function ‘Sarray_new’:
sarray-read.c:302:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T));
               ^
sarray-read.c:368:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2,
               ^
sarray-read.c:434:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T),
               ^
sarray-read.c:526:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T));
               ^
sarray-read.c:653:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,
               ^
sarray-read.c: In function ‘Elt_dump_list’:
sarray-read.c:1667:9: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%d..%d:%u\t",elt->querystart,elt->queryend,elt->positions[k]);
         ^
sarray-read.c: In function ‘Elt_dump’:
sarray-read.c:1682:12: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%d..%d:%u\n",elt->querystart,elt->queryend,elt->positions[k]);
            ^
sarray-read.c: In function ‘collect_elt_matches’:
sarray-read.c:2170:11: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
     array = Uintlist_to_array(&n,difflist);
           ^
sarray-read.c:2442:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:2442:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
             ^
sarray-read.c:2456:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          /*ambcoords_donor*/NULL,ambcoords,
                                  ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:2499:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:2499:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
             ^
sarray-read.c:2513:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          ambcoords,/*ambcoords_acceptor*/NULL,
          ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:2643:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:2643:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
             ^
sarray-read.c:2656:36: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
            /*ambcoords_donor*/NULL,ambcoords,
                                    ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:2699:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:2699:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
             ^
sarray-read.c:2712:12: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
            ambcoords,/*ambcoords_acceptor*/NULL,
            ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:2752:11: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
     array = Uintlist_to_array(&n,difflist);
           ^
sarray-read.c:3024:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:3024:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
             ^
sarray-read.c:3038:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          /*ambcoords_donor*/NULL,ambcoords,
                                  ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:3082:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:3082:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
             ^
sarray-read.c:3096:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          ambcoords,/*ambcoords_acceptor*/NULL,
          ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:3217:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:3217:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor));
             ^
sarray-read.c:3231:34: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          /*ambcoords_donor*/NULL,ambcoords,
                                  ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
sarray-read.c:3274:30: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
                              ^
In file included from genomicpos.h:9:0,
                 from genome.h:8,
                 from sarray-read.h:5,
                 from sarray-read.c:9:
uint8list.h:11:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Uint8list_push (T list, UINT8 x);
 ^
sarray-read.c:3274:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor));
             ^
sarray-read.c:3288:10: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types]
          ambcoords,/*ambcoords_acceptor*/NULL,
          ^
In file included from sarray-read.c:24:0:
stage3hr.h:292:1: note: expected ‘Uint8list_T {aka struct Uint8list_T *}’ but argument is of type ‘Uintlist_T {aka struct Uintlist_T *}’
 Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
 ^
mv -f .deps/uniqscanl-sarray-read.Tpo .deps/uniqscanl-sarray-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage1hr.o -MD -MP -MF .deps/uniqscanl-stage1hr.Tpo -c -o uniqscanl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c
stage1hr.c: In function ‘find_singlesplices_plus’:
stage1hr.c:6629:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n",
                     ^
stage1hr.c:6629:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6629:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(stderr,"Unexpected: Neither donor genomicstart %u(..%u), %d nor acceptor genomicstart %u(..%u), %d equals segmenti_left %u\n",
                     ^
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 6 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 7 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:6768:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 9 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c: In function ‘find_singlesplices_minus’:
stage1hr.c:7145:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n",
                     ^
stage1hr.c:7145:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:7145:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:7284:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
      fprintf(stderr,"Unexpected: Neither donor left %u nor acceptor left %u equals segmenti_left %u\n",
                     ^
stage1hr.c:7284:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
stage1hr.c:7284:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/uniqscanl-stage1hr.Tpo .deps/uniqscanl-stage1hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-resulthr.o -MD -MP -MF .deps/uniqscanl-resulthr.Tpo -c -o uniqscanl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c
mv -f .deps/uniqscanl-resulthr.Tpo .deps/uniqscanl-resulthr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-datadir.o -MD -MP -MF .deps/uniqscanl-datadir.Tpo -c -o uniqscanl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/uniqscanl-datadir.Tpo .deps/uniqscanl-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt.o -MD -MP -MF .deps/uniqscanl-getopt.Tpo -c -o uniqscanl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/uniqscanl-getopt.Tpo .deps/uniqscanl-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt1.o -MD -MP -MF .deps/uniqscanl-getopt1.Tpo -c -o uniqscanl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/uniqscanl-getopt1.Tpo .deps/uniqscanl-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uniqscan.o -MD -MP -MF .deps/uniqscanl-uniqscan.Tpo -c -o uniqscanl-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c
mv -f .deps/uniqscanl-uniqscan.Tpo .deps/uniqscanl-uniqscan.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx  -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3    -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o  -lz -lbz2 -lm 
libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-except.o -MD -MP -MF .deps/snpindex-except.Tpo -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/snpindex-except.Tpo .deps/snpindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-assert.o -MD -MP -MF .deps/snpindex-assert.Tpo -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/snpindex-assert.Tpo .deps/snpindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-mem.o -MD -MP -MF .deps/snpindex-mem.Tpo -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/snpindex-mem.Tpo .deps/snpindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-intlist.o -MD -MP -MF .deps/snpindex-intlist.Tpo -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/snpindex-intlist.Tpo .deps/snpindex-intlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-list.o -MD -MP -MF .deps/snpindex-list.Tpo -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/snpindex-list.Tpo .deps/snpindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-littleendian.o -MD -MP -MF .deps/snpindex-littleendian.Tpo -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/snpindex-littleendian.Tpo .deps/snpindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bigendian.o -MD -MP -MF .deps/snpindex-bigendian.Tpo -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/snpindex-bigendian.Tpo .deps/snpindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-univinterval.o -MD -MP -MF .deps/snpindex-univinterval.Tpo -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/snpindex-univinterval.Tpo .deps/snpindex-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-interval.o -MD -MP -MF .deps/snpindex-interval.Tpo -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/snpindex-interval.Tpo .deps/snpindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-uintlist.o -MD -MP -MF .deps/snpindex-uintlist.Tpo -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/snpindex-uintlist.Tpo .deps/snpindex-uintlist.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-stopwatch.o -MD -MP -MF .deps/snpindex-stopwatch.Tpo -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/snpindex-stopwatch.Tpo .deps/snpindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-access.o -MD -MP -MF .deps/snpindex-access.Tpo -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/snpindex-access.Tpo .deps/snpindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read-univ.o -MD -MP -MF .deps/snpindex-iit-read-univ.Tpo -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/snpindex-iit-read-univ.Tpo .deps/snpindex-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read.o -MD -MP -MF .deps/snpindex-iit-read.Tpo -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/snpindex-iit-read.Tpo .deps/snpindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genomicpos.o -MD -MP -MF .deps/snpindex-genomicpos.Tpo -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/snpindex-genomicpos.Tpo .deps/snpindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress.o -MD -MP -MF .deps/snpindex-compress.Tpo -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/snpindex-compress.Tpo .deps/snpindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress-write.o -MD -MP -MF .deps/snpindex-compress-write.Tpo -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c: In function ‘fill_buffer’:
compress-write.c:73:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
         ^
compress-write.c: In function ‘write_compressed_one’:
compress-write.c:251:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
compress-write.c: In function ‘put_compressed_one’:
compress-write.c:299:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
mv -f .deps/snpindex-compress-write.Tpo .deps/snpindex-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome_hr.o -MD -MP -MF .deps/snpindex-genome_hr.Tpo -c -o snpindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/snpindex-genome_hr.Tpo .deps/snpindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-read.o -MD -MP -MF .deps/snpindex-bitpack64-read.Tpo -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/snpindex-bitpack64-read.Tpo .deps/snpindex-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-write.o -MD -MP -MF .deps/snpindex-bitpack64-write.Tpo -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/snpindex-bitpack64-write.Tpo .deps/snpindex-bitpack64-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb.o -MD -MP -MF .deps/snpindex-indexdb.Tpo -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/snpindex-indexdb.Tpo .deps/snpindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb-write.o -MD -MP -MF .deps/snpindex-indexdb-write.Tpo -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c: In function ‘check_offsets_from_bitpack’:
indexdb-write.c:2494:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u.  Please inform twu@gene.com\n",
                 ^
indexdb-write.c:2494:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
indexdb-write.c:2494:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
indexdb-write.c: In function ‘check_offsets_from_gammas’:
indexdb-write.c:2726:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                      ^
indexdb-write.c:2737:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                      ^
indexdb-write.c:2760:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
  fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                 ^
indexdb-write.c:2787:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                    ^
indexdb-write.c:2798:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                    ^
indexdb-write.c: In function ‘Indexdb_write_offsets’:
indexdb-write.c:2888:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
   fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T));
                  ^
indexdb-write.c:2895:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part);
                    ^
indexdb-write.c:2972:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
indexdb-write.c:3094:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]);
                      ^
indexdb-write.c:3127:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                      ^
indexdb-write.c:3171:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                      ^
indexdb-write.c: In function ‘compute_positions_in_file’:
indexdb-write.c:3371:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
indexdb-write.c: In function ‘compute_positions_in_memory’:
indexdb-write.c:3601:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
mv -f .deps/snpindex-indexdb-write.Tpo .deps/snpindex-indexdb-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-chrom.o -MD -MP -MF .deps/snpindex-chrom.Tpo -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/snpindex-chrom.Tpo .deps/snpindex-chrom.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-md5.o -MD -MP -MF .deps/snpindex-md5.Tpo -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/snpindex-md5.Tpo .deps/snpindex-md5.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bzip2.o -MD -MP -MF .deps/snpindex-bzip2.Tpo -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
mv -f .deps/snpindex-bzip2.Tpo .deps/snpindex-bzip2.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-sequence.o -MD -MP -MF .deps/snpindex-sequence.Tpo -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/snpindex-sequence.Tpo .deps/snpindex-sequence.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome.o -MD -MP -MF .deps/snpindex-genome.Tpo -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10292:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left);
                    ^
genome.c:10392:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
genome.c: In function ‘fill_buffer’:
genome.c:10185:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘genomecomp_read_current’:
genome.c:377:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(this->fd,buffer,4);
   ^
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10320:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10417:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(genomealt->fd,gbuffer1,length);
       ^
genome.c: In function ‘Genome_get_char’:
genome.c:10583:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer1,/*length*/1);
       ^
genome.c: In function ‘Genome_ntcounts’:
genome.c:10857:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
       read(this->fd,gbuffer,length);
       ^
mv -f .deps/snpindex-genome.Tpo .deps/snpindex-genome.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-datadir.o -MD -MP -MF .deps/snpindex-datadir.Tpo -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/snpindex-datadir.Tpo .deps/snpindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt.o -MD -MP -MF .deps/snpindex-getopt.Tpo -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/snpindex-getopt.Tpo .deps/snpindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt1.o -MD -MP -MF .deps/snpindex-getopt1.Tpo -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/snpindex-getopt1.Tpo .deps/snpindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-snpindex.o -MD -MP -MF .deps/snpindex-snpindex.Tpo -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c
snpindex.c: In function ‘merge_positions8’:
snpindex.c:889:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘UINT8 {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Problem: saw duplicate positions %lu in oligo %s\n",*ptr1,nt);
                      ^
snpindex.c: In function ‘main’:
snpindex.c:1143:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(stderr,"Allocating %lu*3*%lu bytes for compressed genome\n",nblocks,sizeof(Genomecomp_T));
                  ^
snpindex.c:1270:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
   fprintf(stderr,"Writing %lu offsets with %u total positions\n",oligospace+1,offsets[oligospace]);
                  ^
mv -f .deps/snpindex-snpindex.Tpo .deps/snpindex-snpindex.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3    -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o  -lz -lbz2 -lm 
libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o  -lz -lbz2 -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-except.o -MD -MP -MF .deps/cmetindex-except.Tpo -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/cmetindex-except.Tpo .deps/cmetindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-assert.o -MD -MP -MF .deps/cmetindex-assert.Tpo -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/cmetindex-assert.Tpo .deps/cmetindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-mem.o -MD -MP -MF .deps/cmetindex-mem.Tpo -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/cmetindex-mem.Tpo .deps/cmetindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-littleendian.o -MD -MP -MF .deps/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/cmetindex-littleendian.Tpo .deps/cmetindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bigendian.o -MD -MP -MF .deps/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/cmetindex-bigendian.Tpo .deps/cmetindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genomicpos.o -MD -MP -MF .deps/cmetindex-genomicpos.Tpo -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/cmetindex-genomicpos.Tpo .deps/cmetindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-stopwatch.o -MD -MP -MF .deps/cmetindex-stopwatch.Tpo -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/cmetindex-stopwatch.Tpo .deps/cmetindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-access.o -MD -MP -MF .deps/cmetindex-access.Tpo -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/cmetindex-access.Tpo .deps/cmetindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-univinterval.o -MD -MP -MF .deps/cmetindex-univinterval.Tpo -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/cmetindex-univinterval.Tpo .deps/cmetindex-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-interval.o -MD -MP -MF .deps/cmetindex-interval.Tpo -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/cmetindex-interval.Tpo .deps/cmetindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read-univ.o -MD -MP -MF .deps/cmetindex-iit-read-univ.Tpo -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/cmetindex-iit-read-univ.Tpo .deps/cmetindex-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read.o -MD -MP -MF .deps/cmetindex-iit-read.Tpo -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/cmetindex-iit-read.Tpo .deps/cmetindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress.o -MD -MP -MF .deps/cmetindex-compress.Tpo -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/cmetindex-compress.Tpo .deps/cmetindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress-write.o -MD -MP -MF .deps/cmetindex-compress-write.Tpo -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c: In function ‘fill_buffer’:
compress-write.c:73:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
         ^
compress-write.c: In function ‘write_compressed_one’:
compress-write.c:251:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
compress-write.c: In function ‘put_compressed_one’:
compress-write.c:299:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
mv -f .deps/cmetindex-compress-write.Tpo .deps/cmetindex-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genome_hr.o -MD -MP -MF .deps/cmetindex-genome_hr.Tpo -c -o cmetindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/cmetindex-genome_hr.Tpo .deps/cmetindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-read.o -MD -MP -MF .deps/cmetindex-bitpack64-read.Tpo -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/cmetindex-bitpack64-read.Tpo .deps/cmetindex-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-write.o -MD -MP -MF .deps/cmetindex-bitpack64-write.Tpo -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/cmetindex-bitpack64-write.Tpo .deps/cmetindex-bitpack64-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb.o -MD -MP -MF .deps/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/cmetindex-indexdb.Tpo .deps/cmetindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb-write.o -MD -MP -MF .deps/cmetindex-indexdb-write.Tpo -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c: In function ‘check_offsets_from_bitpack’:
indexdb-write.c:2494:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u.  Please inform twu@gene.com\n",
                 ^
indexdb-write.c:2494:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
indexdb-write.c:2494:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
indexdb-write.c: In function ‘check_offsets_from_gammas’:
indexdb-write.c:2726:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                      ^
indexdb-write.c:2737:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                      ^
indexdb-write.c:2760:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
  fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                 ^
indexdb-write.c:2787:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                    ^
indexdb-write.c:2798:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                    ^
indexdb-write.c: In function ‘Indexdb_write_offsets’:
indexdb-write.c:2888:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
   fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T));
                  ^
indexdb-write.c:2895:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part);
                    ^
indexdb-write.c:2972:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
indexdb-write.c:3094:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]);
                      ^
indexdb-write.c:3127:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                      ^
indexdb-write.c:3171:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                      ^
indexdb-write.c: In function ‘compute_positions_in_file’:
indexdb-write.c:3371:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
indexdb-write.c: In function ‘compute_positions_in_memory’:
indexdb-write.c:3601:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
mv -f .deps/cmetindex-indexdb-write.Tpo .deps/cmetindex-indexdb-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmet.o -MD -MP -MF .deps/cmetindex-cmet.Tpo -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
mv -f .deps/cmetindex-cmet.Tpo .deps/cmetindex-cmet.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-list.o -MD -MP -MF .deps/cmetindex-list.Tpo -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/cmetindex-list.Tpo .deps/cmetindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-datadir.o -MD -MP -MF .deps/cmetindex-datadir.Tpo -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/cmetindex-datadir.Tpo .deps/cmetindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt.o -MD -MP -MF .deps/cmetindex-getopt.Tpo -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/cmetindex-getopt.Tpo .deps/cmetindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt1.o -MD -MP -MF .deps/cmetindex-getopt1.Tpo -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/cmetindex-getopt1.Tpo .deps/cmetindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmetindex.o -MD -MP -MF .deps/cmetindex-cmetindex.Tpo -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c
mv -f .deps/cmetindex-cmetindex.Tpo .deps/cmetindex-cmetindex.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3    -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o  -lm 
libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o  -lm -pthread
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-except.o -MD -MP -MF .deps/atoiindex-except.Tpo -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/atoiindex-except.Tpo .deps/atoiindex-except.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-assert.o -MD -MP -MF .deps/atoiindex-assert.Tpo -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/atoiindex-assert.Tpo .deps/atoiindex-assert.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-mem.o -MD -MP -MF .deps/atoiindex-mem.Tpo -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/atoiindex-mem.Tpo .deps/atoiindex-mem.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-littleendian.o -MD -MP -MF .deps/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:17:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:34:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:47:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
littleendian.c:53:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
mv -f .deps/atoiindex-littleendian.Tpo .deps/atoiindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bigendian.o -MD -MP -MF .deps/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:285:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,4);
   ^
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:527:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   write(fd,buf,8);
   ^
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:781:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(fd,buf,8);
   ^
mv -f .deps/atoiindex-bigendian.Tpo .deps/atoiindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genomicpos.o -MD -MP -MF .deps/atoiindex-genomicpos.Tpo -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/atoiindex-genomicpos.Tpo .deps/atoiindex-genomicpos.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-stopwatch.o -MD -MP -MF .deps/atoiindex-stopwatch.Tpo -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/atoiindex-stopwatch.Tpo .deps/atoiindex-stopwatch.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:61:7: warning: implicit declaration of function ‘stat64’ [-Wimplicit-function-declaration]
   if (stat64(filename,&sb) == 0) {
       ^
In file included from access.c:41:0:
access.c: In function ‘Access_allocated’:
littleendian.h:20:29: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp)
                             ^
access.c:235:5: note: in expansion of macro ‘FREAD_UINTS’
     FREAD_UINTS(memory,(*len)/eltsize,fp);
     ^
littleendian.h:23:30: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8S(a,n,fp) fread(a,sizeof(UINT8),n,fp)
                              ^
access.c:237:5: note: in expansion of macro ‘FREAD_UINT8S’
     FREAD_UINT8S(memory,(*len)/eltsize,fp);
     ^
mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-univinterval.o -MD -MP -MF .deps/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
univinterval.c: In function ‘Univinterval_print’:
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
   printf("%lu %lu %d",this->low,this->high,this->type);
          ^
univinterval.c:71:10: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
mv -f .deps/atoiindex-univinterval.Tpo .deps/atoiindex-univinterval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-interval.o -MD -MP -MF .deps/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/atoiindex-interval.Tpo .deps/atoiindex-interval.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read-univ.o -MD -MP -MF .deps/atoiindex-iit-read-univ.Tpo -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
iit-read-univ.c: In function ‘Univ_IIT_dump’:
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf(" %lu..%lu",startpos,endpos);
            ^
iit-read-univ.c:507:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_table’:
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
     printf("%lu..%lu\t",startpos,endpos);
            ^
iit-read-univ.c:544:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c: In function ‘Univ_IIT_dump_contigs’:
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
       printf("%lu..%lu\t",startpos+1U,endpos+1U);
              ^
iit-read-univ.c:694:14: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",endpos+1U,startpos+1U);
         ^
iit-read-univ.c:700:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("%lu..%lu\t",startpos+1U,endpos+1U);
         ^
iit-read-univ.c:703:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:873:2: note: in expansion of macro ‘FREAD_UINT’
  FREAD_UINT(&uint4,fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:875:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].a),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:876:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].b),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:877:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].leftindex),fp);
  ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:878:2: note: in expansion of macro ‘FREAD_INT’
  FREAD_INT(&(new->nodes[i].rightindex),fp);
  ^
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:920:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].low),fp);
       ^
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read-univ.c:921:7: note: in expansion of macro ‘FREAD_UINT8’
       FREAD_UINT8(&(new->intervals[i].high),fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:922:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:927:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:929:7: note: in expansion of macro ‘FREAD_UINT’
       FREAD_UINT(&uint4,fp);
       ^
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read-univ.c:931:7: note: in expansion of macro ‘FREAD_INT’
       FREAD_INT(&(new->intervals[i].type),fp);
       ^
iit-read-univ.c: In function ‘read_words’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:991:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1213:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read-univ.c:1217:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1221:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read-univ.c:1225:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
   ^
iit-read-univ.c:1229:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read-univ.c:11:0:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read-univ.c:1073:3: note: in expansion of macro ‘FREAD_UINT’
   FREAD_UINT(&length,fp);
   ^
mv -f .deps/atoiindex-iit-read-univ.Tpo .deps/atoiindex-iit-read-univ.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read.o -MD -MP -MF .deps/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2237:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&version,fp);
     ^
iit-read.c: In function ‘IIT_read’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2495:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_tree’:
iit-read.c:1604:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
  ^
iit-read.c:1605:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
  ^
iit-read.c:1606:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
  ^
iit-read.c:1607:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
  ^
iit-read.c:1608:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
  ^
iit-read.c: In function ‘read_intervals’:
iit-read.c:1689:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1690:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
       ^
iit-read.c:1692:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
  ^
iit-read.c:1696:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
       ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘read_words’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1785:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1791:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
iit-read.c: In function ‘read_annotations’:
iit-read.c:2141:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
   ^
iit-read.c:2147:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2152:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2163:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->labels,new->label_length*sizeof(char));
   ^
iit-read.c:2169:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
     ^
iit-read.c:2174:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
     ^
iit-read.c:2185:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
   read(new->fd,new->annotations,new->annot_length*sizeof(char));
   ^
In file included from iit-read.c:12:0:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:17:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
                         ^
iit-read.c:2898:5: note: in expansion of macro ‘FREAD_INT’
     FREAD_INT(&new->version,fp);
     ^
iit-read.c: In function ‘read_words_debug’:
littleendian.h:22:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
                           ^
iit-read.c:1913:5: note: in expansion of macro ‘FREAD_UINT8’
     FREAD_UINT8(&length8,fp);
     ^
littleendian.h:18:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
                          ^
iit-read.c:1918:5: note: in expansion of macro ‘FREAD_UINT’
     FREAD_UINT(&length,fp);
     ^
mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress.o -MD -MP -MF .deps/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c
mv -f .deps/atoiindex-compress.Tpo .deps/atoiindex-compress.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress-write.o -MD -MP -MF .deps/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
compress-write.c: In function ‘fill_buffer’:
compress-write.c:73:9: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i);
         ^
compress-write.c: In function ‘write_compressed_one’:
compress-write.c:251:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
compress-write.c: In function ‘put_compressed_one’:
compress-write.c:299:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Don't recognize character %c at position %lu.  Using N instead\n",
                 ^
mv -f .deps/atoiindex-compress-write.Tpo .deps/atoiindex-compress-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genome_hr.o -MD -MP -MF .deps/atoiindex-genome_hr.Tpo -c -o atoiindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c
mv -f .deps/atoiindex-genome_hr.Tpo .deps/atoiindex-genome_hr.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-read.o -MD -MP -MF .deps/atoiindex-bitpack64-read.Tpo -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
mv -f .deps/atoiindex-bitpack64-read.Tpo .deps/atoiindex-bitpack64-read.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-write.o -MD -MP -MF .deps/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c
mv -f .deps/atoiindex-bitpack64-write.Tpo .deps/atoiindex-bitpack64-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘Indexdb_offsets_from_bitpack’:
indexdb.c:1934:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘Indexdb_offsets_from_gammas’:
indexdb.c:2026:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Allocating memory (%lu words) for offsets, kmer %d...",oligospace+1UL,
                    ^
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1842:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
     read(positions_fd,buffer,4);
     ^
mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb-write.o -MD -MP -MF .deps/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c
indexdb-write.c: In function ‘check_offsets_from_bitpack’:
indexdb-write.c:2494:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Problem with bitpack at oligo %lu+%d = %lu: %u != %u.  Please inform twu@gene.com\n",
                 ^
indexdb-write.c:2494:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
indexdb-write.c:2494:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
indexdb-write.c: In function ‘check_offsets_from_gammas’:
indexdb-write.c:2726:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                      ^
indexdb-write.c:2737:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                      ^
indexdb-write.c:2760:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
  fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                 ^
indexdb-write.c:2787:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Problem with gammaptrs at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                    ^
indexdb-write.c:2798:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
     fprintf(stderr,"Problem with offsetscomp at oligo %lu: %u != %u.  Please inform twu@gene.com\n",
                    ^
indexdb-write.c: In function ‘Indexdb_write_offsets’:
indexdb-write.c:2888:18: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
   fprintf(stderr,"Allocating %lu*%lu bytes for offsets\n",oligospace+1UL,sizeof(Positionsptr_T));
                  ^
indexdb-write.c:2895:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
     fprintf(stderr,"Unable to allocate %lu bytes of memory, needed to build offsets with %d-mers\n",oligospace+1UL,index1part);
                    ^
indexdb-write.c:2972:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
indexdb-write.c:3094:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘Oligospace_T {aka long long unsigned int}’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets to file with total of %u k-mers...",oligospace+1,offsets[oligospace]);
                      ^
indexdb-write.c:3127:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets compressed via gammas to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                      ^
indexdb-write.c:3171:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
       fprintf(stderr,"Writing %lu offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1UL,offsets[oligospace]);
                      ^
indexdb-write.c: In function ‘compute_positions_in_file’:
indexdb-write.c:3371:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
indexdb-write.c: In function ‘compute_positions_in_memory’:
indexdb-write.c:3601:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘Univcoord_T {aka long long unsigned int}’ [-Wformat=]
  fprintf(stderr,"Bad character %c at position %lu\n",c,position);
                 ^
mv -f .deps/atoiindex-indexdb-write.Tpo .deps/atoiindex-indexdb-write.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoi.o -MD -MP -MF .deps/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
mv -f .deps/atoiindex-atoi.Tpo .deps/atoiindex-atoi.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-list.o -MD -MP -MF .deps/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/atoiindex-list.Tpo .deps/atoiindex-list.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-datadir.o -MD -MP -MF .deps/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/atoiindex-datadir.Tpo .deps/atoiindex-datadir.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt.o -MD -MP -MF .deps/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/atoiindex-getopt.Tpo .deps/atoiindex-getopt.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt1.o -MD -MP -MF .deps/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/atoiindex-getopt1.Tpo .deps/atoiindex-getopt1.Po
gcc -DHAVE_CONFIG_H -I.     -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoiindex.o -MD -MP -MF .deps/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c
mv -f .deps/atoiindex-atoiindex.Tpo .deps/atoiindex-atoiindex.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3    -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o  -lm 
libtool: link: gcc -pthread -DGMAPDB=\"/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o  -lm -pthread
make[3]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/src'
 /bin/mkdir -p '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin'
libtool: install: /usr/bin/install -c gmap /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/gmap
libtool: install: /usr/bin/install -c gmapl /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/gmapl
libtool: install: /usr/bin/install -c get-genome /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/get-genome
libtool: install: /usr/bin/install -c gmapindex /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/gmapindex
libtool: install: /usr/bin/install -c iit_store /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/iit_store
libtool: install: /usr/bin/install -c iit_get /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/iit_get
libtool: install: /usr/bin/install -c iit_dump /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/iit_dump
libtool: install: /usr/bin/install -c gsnap /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/gsnap
libtool: install: /usr/bin/install -c gsnapl /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/gsnapl
libtool: install: /usr/bin/install -c uniqscan /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/uniqscan
libtool: install: /usr/bin/install -c uniqscanl /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/uniqscanl
libtool: install: /usr/bin/install -c snpindex /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/snpindex
libtool: install: /usr/bin/install -c cmetindex /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/cmetindex
libtool: install: /usr/bin/install -c atoiindex /home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin/atoiindex
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/src'
make[2]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/src'
Making install in util
make[2]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/util'
cp gmap_compress.pl gmap_compress
chmod +x gmap_compress
cp gmap_uncompress.pl gmap_uncompress
chmod +x gmap_uncompress
cp gmap_process.pl gmap_process
chmod +x gmap_process
cp gmap_setup.pl gmap_setup
chmod +x gmap_setup
cp gmap_build.pl gmap_build
chmod +x gmap_build
cp gmap_reassemble.pl gmap_reassemble
chmod +x gmap_reassemble
cp md_coords.pl md_coords
chmod +x md_coords
cp fa_coords.pl fa_coords
chmod +x fa_coords
cp psl_splicesites.pl psl_splicesites
chmod +x psl_splicesites
cp psl_introns.pl psl_introns
chmod +x psl_introns
cp psl_genes.pl psl_genes
chmod +x psl_genes
cp gtf_splicesites.pl gtf_splicesites
chmod +x gtf_splicesites
cp gtf_introns.pl gtf_introns
chmod +x gtf_introns
cp gtf_genes.pl gtf_genes
chmod +x gtf_genes
cp gff3_splicesites.pl gff3_splicesites
chmod +x gff3_splicesites
cp gff3_introns.pl gff3_introns
chmod +x gff3_introns
cp gff3_genes.pl gff3_genes
chmod +x gff3_genes
cp dbsnp_iit.pl dbsnp_iit
chmod +x dbsnp_iit
cp gvf_iit.pl gvf_iit
chmod +x gvf_iit
cp vcf_iit.pl vcf_iit
chmod +x vcf_iit
make[3]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/util'
 /bin/mkdir -p '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin'
 /usr/bin/install -c gmap_compress gmap_uncompress gmap_process gmap_setup gmap_build gmap_reassemble md_coords fa_coords psl_splicesites psl_introns psl_genes gtf_splicesites gtf_introns gtf_genes gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/../inst/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/util'
make[2]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/util'
Making install in tests
make[2]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/tests'
make[3]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/tests'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/tests'
make[2]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap/tests'
make[2]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap'
make[3]: Entering directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap'
make[2]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap'
make[1]: Leaving directory '/home/biocbuild/bbs-3.7-bioc/meat/gmapR/src/gmap'
installing to /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function from function ‘directory’ in package ‘gmapR’
Creating a generic function for ‘bamPaths’ from package ‘Rsamtools’ in package ‘gmapR’
Note: ... may be used in an incorrect context 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gmapR)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("gmapR") || stop("unable to load gmapR package")
Loading required package: gmapR
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] TRUE
> gmapR:::.test()
NOTE: genome 'hg19.p53' already exists, not overwriting
Loading required package: BSgenome
Loading required package: rtracklayer
writing chrI sequence to file ... OK
writing chrII sequence to file ... OK
writing chrIII sequence to file ... OK
writing chrIV sequence to file ... OK
writing chrV sequence to file ... OK
writing chrVI sequence to file ... OK
writing chrVII sequence to file ... OK
writing chrVIII sequence to file ... OK
writing chrIX sequence to file ... OK
writing chrX sequence to file ... OK
writing chrXI sequence to file ... OK
writing chrXII sequence to file ... OK
writing chrXIII sequence to file ... OK
writing chrXIV sequence to file ... OK
writing chrXV sequence to file ... OK
writing chrXVI sequence to file ... OK
writing chrM sequence to file ... OK
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//fa_coords  -c chrM -o ./yeast.coords "/tmp/RtmpyVLQLR/gmap_build_fasta6b83285e13f3"
Opening file /tmp/RtmpyVLQLR/gmap_build_fasta6b83285e13f3
  Processed short contigs (<1000000 nt): ...
  Contig chrIV: concatenated at chromosome end: chrIV:1..1531933 (length = 1531933 nt)
  Processed short contigs (<1000000 nt): ..
  Contig chrVII: concatenated at chromosome end: chrVII:1..1090940 (length = 1090940 nt)
  Processed short contigs (<1000000 nt): ....
  Contig chrXII: concatenated at chromosome end: chrXII:1..1078177 (length = 1078177 nt)
  Processed short contigs (<1000000 nt): ..
  Contig chrXV: concatenated at chromosome end: chrXV:1..1091291 (length = 1091291 nt)
  Processed short contigs (<1000000 nt): ..
============================================================
Contig mapping information has been written to file ./yeast.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmap_process  -c ./yeast.coords "/tmp/RtmpyVLQLR/gmap_build_fasta6b83285e13f3" | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex  -d yeast -D . -A -s none
Reading coordinates from file ./yeast.coords
Logging contig chrI at chrI:1..230218 in genome yeast
Logging contig chrII at chrII:1..813184 in genome yeast
Logging contig chrIII at chrIII:1..316620 in genome yeast
Logging contig chrIV at chrIV:1..1531933 in genome yeast
Logging contig chrV at chrV:1..576874 in genome yeast
Logging contig chrVI at chrVI:1..270161 in genome yeast
Logging contig chrVII at chrVII:1..1090940 in genome yeast
Logging contig chrVIII at chrVIII:1..562643 in genome yeast
Logging contig chrIX at chrIX:1..439888 in genome yeast
Logging contig chrX at chrX:1..745751 in genome yeast
Logging contig chrXI at chrXI:1..666816 in genome yeast
Logging contig chrXII at chrXII:1..1078177 in genome yeast
Logging contig chrXIII at chrXIII:1..924431 in genome yeast
Logging contig chrXIV at chrXIV:1..784333 in genome yeast
Logging contig chrXV at chrXV:1..1091291 in genome yeast
Logging contig chrXVI at chrXVI:1..948066 in genome yeast
Logging contig chrM at chrM:1..85779 in genome yeast
chrM is a circular chromosome
Total genomic length = 12157105 bp
Chromosome chrI has universal coordinates 1..230218
Chromosome chrII has universal coordinates 230219..1043402
Chromosome chrIII has universal coordinates 1043403..1360022
Chromosome chrIV has universal coordinates 1360023..2891955
Chromosome chrV has universal coordinates 2891956..3468829
Chromosome chrVI has universal coordinates 3468830..3738990
Chromosome chrVII has universal coordinates 3738991..4829930
Chromosome chrVIII has universal coordinates 4829931..5392573
Chromosome chrIX has universal coordinates 5392574..5832461
Chromosome chrX has universal coordinates 5832462..6578212
Chromosome chrXI has universal coordinates 6578213..7245028
Chromosome chrXII has universal coordinates 7245029..8323205
Chromosome chrXIII has universal coordinates 8323206..9247636
Chromosome chrXIV has universal coordinates 9247637..10031969
Chromosome chrXV has universal coordinates 10031970..11123260
Chromosome chrXVI has universal coordinates 11123261..12071326
Chromosome chrM has universal coordinates 12071327..12157105
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (17 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (17 intervals)
Writing IIT file footer information...done
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmap_process  -c ./yeast.coords "/tmp/RtmpyVLQLR/gmap_build_fasta6b83285e13f3" | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex  -d yeast -F . -D . -G
Genome length is 12242884 nt
Trying to allocate 1147773*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./yeast.coords
Writing contig chrI to universal coordinates 1..230218 in genome yeast
Writing contig chrII to universal coordinates 230219..1043402 in genome yeast
Writing contig chrIII to universal coordinates 1043403..1360022 in genome yeast
Writing contig chrIV to universal coordinates 1360023..2891955 in genome yeast
Writing contig chrV to universal coordinates 2891956..3468829 in genome yeast
Writing contig chrVI to universal coordinates 3468830..3738990 in genome yeast
Writing contig chrVII to universal coordinates 3738991..4829930 in genome yeast
Writing contig chrVIII to universal coordinates 4829931..5392573 in genome yeast
Writing contig chrIX to universal coordinates 5392574..5832461 in genome yeast
Writing contig chrX to universal coordinates 5832462..6578212 in genome yeast
Writing contig chrXI to universal coordinates 6578213..7245028 in genome yeast
Writing contig chrXII to universal coordinates 7245029..8323205 in genome yeast
Writing contig chrXIII to universal coordinates 8323206..9247636 in genome yeast
Writing contig chrXIV to universal coordinates 9247637..10031969 in genome yeast
Writing contig chrXV to universal coordinates 10031970..11123260 in genome yeast
Writing contig chrXVI to universal coordinates 11123261..12071326 in genome yeast
Writing contig chrM to universal coordinates 12071327..12157105 in genome yeast
Chromosome chrM is circular.  Copying 12071327..12157105 to 12157106..12242884
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./yeast.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -d yeast -U > ./yeast.genomebits
Running cat ./yeast.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d yeast -F . -D . -O 
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome yeast (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 4080904 k-mers...done
Running cat ./yeast.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d yeast -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is yeast.ref123offsets
  Positions file is yeast.ref123positions
Trying to allocate 4080904*4 bytes of memory...succeeded.  Building positions in memory.
Indexing positions of oligomers in genome yeast (12 bp every 3 bp), position 0
Writing 4080904 genomic positions to file ./yeast.ref123positions ...
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -d yeast -F . -D . -S
SACA_K called with n = 12242885, K = 5, level 0
SACA_K called with n = 3442582, K = 0, level 1
SACA_K called with n = 1091915, K = 0, level 2
SACA_K called with n = 355699, K = 0, level 3
SACA_K called with n = 115942, K = 0, level 4
SACA_K called with n = 37652, K = 0, level 5
SACA_K called with n = 12156, K = 0, level 6
SACA_K called with n = 4037, K = 0, level 7
SACA_K called with n = 1305, K = 0, level 8
Computing lcp...done
Computing saindex...done
Copying files to directory /tmp/RtmpyVLQLR/511874772/yeast
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//fa_coords   -o ./thing.coords "/tmp/RtmpyVLQLR/file6b831df9419f"
Opening file /tmp/RtmpyVLQLR/file6b831df9419f
  Processed short contigs (<1000000 nt): .
============================================================
Contig mapping information has been written to file ./thing.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmap_process  -c ./thing.coords "/tmp/RtmpyVLQLR/file6b831df9419f" | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex  -d thing -D . -A -s none
Reading coordinates from file ./thing.coords
Logging contig sampleDNAStringSet at sampleDNAStringSet:1..2000 in genome thing
Total genomic length = 2000 bp
Chromosome sampleDNAStringSet has universal coordinates 1..2000
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (1 intervals)
Writing IIT file footer information...done
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmap_process  -c ./thing.coords "/tmp/RtmpyVLQLR/file6b831df9419f" | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex  -d thing -F . -D . -G
Genome length is 2000 nt
Trying to allocate 189*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./thing.coords
Writing contig sampleDNAStringSet to universal coordinates 1..2000 in genome thing
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./thing.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -d thing -U > ./thing.genomebits
Running cat ./thing.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d thing -F . -D . -O 
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome thing (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 663 k-mers...done
Running cat ./thing.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d thing -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is thing.ref123offsets
  Positions file is thing.ref123positions
Trying to allocate 663*4 bytes of memory...succeeded.  Building positions in memory.
Indexing positions of oligomers in genome thing (12 bp every 3 bp), position 0
Writing 663 genomic positions to file ./thing.ref123positions ...
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -d thing -F . -D . -S
SACA_K called with n = 2001, K = 5, level 0
SACA_K called with n = 579, K = 0, level 1
Computing lcp...done
Computing saindex...done
Copying files to directory /tmp/RtmpyVLQLR/871805021/thing
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//fa_coords   -o ./testGenome.coords "/tmp/RtmpyVLQLR/file6b8368d09066"
Opening file /tmp/RtmpyVLQLR/file6b8368d09066
  Processed short contigs (<1000000 nt): ..
============================================================
Contig mapping information has been written to file ./testGenome.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmap_process  -c ./testGenome.coords "/tmp/RtmpyVLQLR/file6b8368d09066" | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex  -d testGenome -D . -A -s none
Reading coordinates from file ./testGenome.coords
Logging contig testA at testA:1..26 in genome testGenome
Logging contig testB at testB:1..13 in genome testGenome
Total genomic length = 39 bp
Chromosome testA has universal coordinates 1..26
Chromosome testB has universal coordinates 27..39
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (2 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (2 intervals)
Writing IIT file footer information...done
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmap_process  -c ./testGenome.coords "/tmp/RtmpyVLQLR/file6b8368d09066" | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex  -d testGenome -F . -D . -G
Genome length is 39 nt
Trying to allocate 6*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./testGenome.coords
Writing contig testA to universal coordinates 1..26 in genome testGenome
Writing contig testB to universal coordinates 27..39 in genome testGenome
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./testGenome.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -d testGenome -U > ./testGenome.genomebits
Running cat ./testGenome.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d testGenome -F . -D . -O 
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome testGenome (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 6 k-mers...done
Running cat ./testGenome.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d testGenome -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is testGenome.ref123offsets
  Positions file is testGenome.ref123positions
Trying to allocate 6*4 bytes of memory...succeeded.  Building positions in memory.
Indexing positions of oligomers in genome testGenome (12 bp every 3 bp), position 0
Writing 6 genomic positions to file ./testGenome.ref123positions ...
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -d testGenome -F . -D . -S
SACA_K called with n = 40, K = 5, level 0
Computing lcp...done
Computing saindex...done
Copying files to directory /tmp/RtmpyVLQLR/file6b8317f4f454/testGenome
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Finished reading FASTA file -- total entries: 4918
Maximum coordinate: 1968875
Total label length: 29508 + 4918 separators
Total annotation length: 20152 + 4918 separators
Saw 1 distinct divisions/chromosomes
Saw 3 distinct tags/types
Writing IIT file header information...done
Processing null division/chromosome...sorting...writing...done (0 intervals)
Processing division/chromosome chr17...sorting...writing...done (4918 intervals)
Writing IIT file footer information...done
NOTE: genome 'hg19.p53' already exists, not overwriting
Creating directory /tmp/RtmpyVLQLR/66073
writing chrI sequence to file ... OK
writing chrII sequence to file ... OK
writing chrIII sequence to file ... OK
writing chrIV sequence to file ... OK
writing chrV sequence to file ... OK
writing chrVI sequence to file ... OK
writing chrVII sequence to file ... OK
writing chrVIII sequence to file ... OK
writing chrIX sequence to file ... OK
writing chrX sequence to file ... OK
writing chrXI sequence to file ... OK
writing chrXII sequence to file ... OK
writing chrXIII sequence to file ... OK
writing chrXIV sequence to file ... OK
writing chrXV sequence to file ... OK
writing chrXVI sequence to file ... OK
writing chrM sequence to file ... OK
-k flag specified (not as 15), but not -b, so building with base size == kmer size
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//fa_coords  -c chrM -o ./yeast.coords "/tmp/RtmpyVLQLR/gmap_build_fasta6b8354eb5e26"
Opening file /tmp/RtmpyVLQLR/gmap_build_fasta6b8354eb5e26
  Processed short contigs (<1000000 nt): ...
  Contig chrIV: concatenated at chromosome end: chrIV:1..1531933 (length = 1531933 nt)
  Processed short contigs (<1000000 nt): ..
  Contig chrVII: concatenated at chromosome end: chrVII:1..1090940 (length = 1090940 nt)
  Processed short contigs (<1000000 nt): ....
  Contig chrXII: concatenated at chromosome end: chrXII:1..1078177 (length = 1078177 nt)
  Processed short contigs (<1000000 nt): ..
  Contig chrXV: concatenated at chromosome end: chrXV:1..1091291 (length = 1091291 nt)
  Processed short contigs (<1000000 nt): ..
============================================================
Contig mapping information has been written to file ./yeast.coords.
You should look at this file, and edit it if necessary
If everything is okay, you should proceed by running
    make gmapdb
============================================================
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmap_process  -c ./yeast.coords "/tmp/RtmpyVLQLR/gmap_build_fasta6b8354eb5e26" | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex  -d yeast -D . -A -s none
Reading coordinates from file ./yeast.coords
Logging contig chrI at chrI:1..230218 in genome yeast
Logging contig chrII at chrII:1..813184 in genome yeast
Logging contig chrIII at chrIII:1..316620 in genome yeast
Logging contig chrIV at chrIV:1..1531933 in genome yeast
Logging contig chrV at chrV:1..576874 in genome yeast
Logging contig chrVI at chrVI:1..270161 in genome yeast
Logging contig chrVII at chrVII:1..1090940 in genome yeast
Logging contig chrVIII at chrVIII:1..562643 in genome yeast
Logging contig chrIX at chrIX:1..439888 in genome yeast
Logging contig chrX at chrX:1..745751 in genome yeast
Logging contig chrXI at chrXI:1..666816 in genome yeast
Logging contig chrXII at chrXII:1..1078177 in genome yeast
Logging contig chrXIII at chrXIII:1..924431 in genome yeast
Logging contig chrXIV at chrXIV:1..784333 in genome yeast
Logging contig chrXV at chrXV:1..1091291 in genome yeast
Logging contig chrXVI at chrXVI:1..948066 in genome yeast
Logging contig chrM at chrM:1..85779 in genome yeast
chrM is a circular chromosome
Total genomic length = 12157105 bp
Chromosome chrI has universal coordinates 1..230218
Chromosome chrII has universal coordinates 230219..1043402
Chromosome chrIII has universal coordinates 1043403..1360022
Chromosome chrIV has universal coordinates 1360023..2891955
Chromosome chrV has universal coordinates 2891956..3468829
Chromosome chrVI has universal coordinates 3468830..3738990
Chromosome chrVII has universal coordinates 3738991..4829930
Chromosome chrVIII has universal coordinates 4829931..5392573
Chromosome chrIX has universal coordinates 5392574..5832461
Chromosome chrX has universal coordinates 5832462..6578212
Chromosome chrXI has universal coordinates 6578213..7245028
Chromosome chrXII has universal coordinates 7245029..8323205
Chromosome chrXIII has universal coordinates 8323206..9247636
Chromosome chrXIV has universal coordinates 9247637..10031969
Chromosome chrXV has universal coordinates 10031970..11123260
Chromosome chrXVI has universal coordinates 11123261..12071326
Chromosome chrM has universal coordinates 12071327..12157105
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (17 intervals)
Writing IIT file footer information...done
Writing IIT file header information...coordinates require 4 bytes each...done
Processing null division/chromosome...sorting...writing...done (17 intervals)
Writing IIT file footer information...done
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmap_process  -c ./yeast.coords "/tmp/RtmpyVLQLR/gmap_build_fasta6b8354eb5e26" | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex  -d yeast -F . -D . -G
Genome length is 12242884 nt
Trying to allocate 1147773*4 bytes of memory...succeeded.  Building genome in memory.
Reading coordinates from file ./yeast.coords
Writing contig chrI to universal coordinates 1..230218 in genome yeast
Writing contig chrII to universal coordinates 230219..1043402 in genome yeast
Writing contig chrIII to universal coordinates 1043403..1360022 in genome yeast
Writing contig chrIV to universal coordinates 1360023..2891955 in genome yeast
Writing contig chrV to universal coordinates 2891956..3468829 in genome yeast
Writing contig chrVI to universal coordinates 3468830..3738990 in genome yeast
Writing contig chrVII to universal coordinates 3738991..4829930 in genome yeast
Writing contig chrVIII to universal coordinates 4829931..5392573 in genome yeast
Writing contig chrIX to universal coordinates 5392574..5832461 in genome yeast
Writing contig chrX to universal coordinates 5832462..6578212 in genome yeast
Writing contig chrXI to universal coordinates 6578213..7245028 in genome yeast
Writing contig chrXII to universal coordinates 7245029..8323205 in genome yeast
Writing contig chrXIII to universal coordinates 8323206..9247636 in genome yeast
Writing contig chrXIV to universal coordinates 9247637..10031969 in genome yeast
Writing contig chrXV to universal coordinates 10031970..11123260 in genome yeast
Writing contig chrXVI to universal coordinates 11123261..12071326 in genome yeast
Writing contig chrM to universal coordinates 12071327..12157105 in genome yeast
Chromosome chrM is circular.  Copying 12071327..12157105 to 12157106..12242884
A total of 0 non-ACGTNX characters were seen in the genome.
Running cat ./yeast.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -d yeast -U > ./yeast.genomebits
Running cat ./yeast.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d yeast -F . -D . -O 
Note: since base size is equal to the k-mer size 12, offsets will not be compressed
Offset compression types:
Allocating 16777217*4 bytes for offsets
Indexing offsets of oligomers in genome yeast (12 bp every 3 bp), position 0
Writing 16777217 offsets to file with total of 4080904 k-mers...done
Running cat ./yeast.genomecomp | /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -b 12 -k 12 -q 3  -d yeast -F . -D . -P
Looking for index files in directory . (offsets not compressed)
  Offsets file is yeast.ref123offsets
  Positions file is yeast.ref123positions
Trying to allocate 4080904*4 bytes of memory...succeeded.  Building positions in memory.
Indexing positions of oligomers in genome yeast (12 bp every 3 bp), position 0
Writing 4080904 genomic positions to file ./yeast.ref123positions ...
Running /home/biocbuild/bbs-3.7-bioc/R/library/gmapR/usr/bin//gmapindex -d yeast -F . -D . -S
SACA_K called with n = 12242885, K = 5, level 0
SACA_K called with n = 3442582, K = 0, level 1
SACA_K called with n = 1091915, K = 0, level 2
SACA_K called with n = 355699, K = 0, level 3
SACA_K called with n = 115942, K = 0, level 4
SACA_K called with n = 37652, K = 0, level 5
SACA_K called with n = 12156, K = 0, level 6
SACA_K called with n = 4037, K = 0, level 7
SACA_K called with n = 1305, K = 0, level 8
Computing lcp...done
Computing saindex...done
Copying files to directory /tmp/RtmpyVLQLR/66073/yeast
Creating package in /tmp/RtmpyVLQLR/50224/GmapGenome.Scerevisiae.UCSC.sacCer3 


RUNIT TEST PROTOCOL -- Tue Oct 16 00:58:38 2018 
*********************************************** 
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gmapR RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 79.532   3.320 148.152 

name	user	system	elapsed
GmapGenome-class	0.004	0.000	0.001
GmapGenomeDirectory-class	0.004	0.000	0.002
TP53Genome	0.008	0.000	0.025
cmetindex	0	0	0
gmap_build-methods	0	0	0
makeGmapGenomePackage	0.000	0.000	0.001