gmapR 1.1.11
Cory Barr
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR | | Last Changed Rev: 74113 / Revision: 74774 | | Last Changed Date: 2013-03-08 17:04:14 -0800 (Fri, 08 Mar 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gmapR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gmapR' version '1.1.11'
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'gmapR' can be installed ... [242s/252s] OK
* checking installed package size ... NOTE
installed size is 38.2Mb
sub-directories of 1Mb or more:
extdata 5.5Mb
usr 31.7Mb
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/gmapR/libs/i386/gmapR.so':
Found '___stderrp', possibly from 'stderr' (C)
Found '_abort', possibly from 'abort' (C)
Found '_exit', possibly from 'exit' (C)
Found '_printf', possibly from 'printf' (C)
Found '_putchar', possibly from 'putchar' (C)
Found '_puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console. 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [16s/16s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'gmapR_unit_tests.R' [262s/307s]
ERROR
Running the tests in 'tests/gmapR_unit_tests.R' failed.
Last 13 lines of output:
FALSE
Test files with failing tests
test_GmapGenome.R
test_GmapGenome_accessors
Error in gmapR:::.test() : unit tests failed for package gmapR
In addition: Warning message:
%in% between a GRangesList and a GRanges object is deprecated.
Please use 'query %over% subject' instead.
Execution halted
* installing *source* package 'gmapR' ...
** libs
** arch - i386
rm -rf samtools; mkdir samtools
ln -sf /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//i386/libbam.a samtools/libbam.a
for header in /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include/samtools/*.h; do \
ln -sf $header samtools/; \
done
cd gstruct/; \
./configure --enable-static --disable-shared \
--prefix=/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr --includedir=/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct \
--libdir=/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib \
--with-samtools=/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools \
--disable-binaries #\
## does not appear to be a true dependency yet
checking package version... 2012-08-20
checking CONFIG_SITE... ./config.site
loading script ./config.site
checking CFLAGS... not set by user so using default -O3
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
checking target system type... i386-apple-darwin9.8.0
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 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... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking bindir... /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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 and cc understand -c and -o together... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -p
checking the name lister (/usr/bin/nm -p) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -p output from gcc object... ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
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... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
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/libexec/gcc/i686-apple-darwin9/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin9.8.0 dyld
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 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 uniqscan... false
checking for rint in -lm... yes
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... 4
checking size of unsigned long long... 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 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... yes
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... yes
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking gmapdb... /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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... no
checking for samtools library... enabled
checking for samtools... no
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
cd gstruct; \
make install
Making install in src
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/libgstruct_1.0_la-littleendian.Tpo .deps/libgstruct_1.0_la-littleendian.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/libgstruct_1.0_la-bigendian.Tpo .deps/libgstruct_1.0_la-bigendian.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/libgstruct_1.0_la-access.Tpo .deps/libgstruct_1.0_la-access.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/libgstruct_1.0_la-iit-read.Tpo .deps/libgstruct_1.0_la-iit-read.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/libgstruct_1.0_la-genome.Tpo .deps/libgstruct_1.0_la-genome.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/libgstruct_1.0_la-bamtally.Tpo .deps/libgstruct_1.0_la-bamtally.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=link gcc -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/samtools -fPIC -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -version-info 1:0:0 -o libgstruct-1.0.la -rpath /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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-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-bamtally.o libgstruct_1.0_la-datadir.o
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" )
test -z "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib" || ../config/install-sh -c -d "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib"
/bin/sh ../libtool --mode=install /usr/bin/install -c 'libgstruct-1.0.la' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.la'
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.la
libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: chmod 644 /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
libtool: install: ranlib /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.a
----------------------------------------------------------------------
Libraries have been installed in:
/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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 `DYLD_LIBRARY_PATH' environment variable
during execution
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin" || ../config/install-sh -c -d "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin"
test -z "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct" || ../config/install-sh -c -d "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct"
/usr/bin/install -c -m 644 'config.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/config.h'
/usr/bin/install -c -m 644 'fopen.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/fopen.h'
/usr/bin/install -c -m 644 'bool.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/bool.h'
/usr/bin/install -c -m 644 'types.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/types.h'
/usr/bin/install -c -m 644 'except.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/except.h'
/usr/bin/install -c -m 644 'assert.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/assert.h'
/usr/bin/install -c -m 644 'mem.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/mem.h'
/usr/bin/install -c -m 644 'intlistdef.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/intlistdef.h'
/usr/bin/install -c -m 644 'intlist.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/intlist.h'
/usr/bin/install -c -m 644 'listdef.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/listdef.h'
/usr/bin/install -c -m 644 'list.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/list.h'
/usr/bin/install -c -m 644 'littleendian.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/littleendian.h'
/usr/bin/install -c -m 644 'bigendian.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/bigendian.h'
/usr/bin/install -c -m 644 'interval.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/interval.h'
/usr/bin/install -c -m 644 'uintlist.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/uintlist.h'
/usr/bin/install -c -m 644 'stopwatch.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/stopwatch.h'
/usr/bin/install -c -m 644 'access.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/access.h'
/usr/bin/install -c -m 644 'iitdef.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/iitdef.h'
/usr/bin/install -c -m 644 'iit-read.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/iit-read.h'
/usr/bin/install -c -m 644 'chrom.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/chrom.h'
/usr/bin/install -c -m 644 'genomicpos.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/genomicpos.h'
/usr/bin/install -c -m 644 'md5.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/md5.h'
/usr/bin/install -c -m 644 'complement.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/complement.h'
/usr/bin/install -c -m 644 'sequence.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/sequence.h'
/usr/bin/install -c -m 644 'genome.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/genome.h'
/usr/bin/install -c -m 644 'uinttable.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/uinttable.h'
/usr/bin/install -c -m 644 'table.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/table.h'
/usr/bin/install -c -m 644 'chrnum.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/chrnum.h'
/usr/bin/install -c -m 644 'bamread.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/bamread.h'
/usr/bin/install -c -m 644 'samread.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/samread.h'
/usr/bin/install -c -m 644 'parserange.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/parserange.h'
/usr/bin/install -c -m 644 'tableuint.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/tableuint.h'
/usr/bin/install -c -m 644 'iit-write.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/iit-write.h'
/usr/bin/install -c -m 644 'ucharlist.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/ucharlist.h'
/usr/bin/install -c -m 644 'bamtally.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/bamtally.h'
/usr/bin/install -c -m 644 'datadir.h' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include/gstruct/datadir.h'
test -z "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/pkgconfig" || ../config/install-sh -c -d "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/pkgconfig"
/usr/bin/install -c -m 644 '../lib/gstruct-1.0.pc' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/pkgconfig/gstruct-1.0.pc'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include -g -fPIC -g -O2 -Wall -pedantic -c bamreader.c -o bamreader.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include -g -fPIC -g -O2 -Wall -pedantic -c bamtally.c -o bamtally.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include -g -fPIC -g -O2 -Wall -pedantic -c iit.c -o iit.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include -g -fPIC -g -O2 -Wall -pedantic -c variantsummary.c -o variantsummary.o
In file included from variantsummary.c:5:
bytestream.h: In function 'read_string':
bytestream.h:20: warning: pointer targets in initialization differ in signedness
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/include -I/usr/local/include -g -fPIC -g -O2 -Wall -pedantic -c R_init_gmapR.c -o R_init_gmapR.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o R_init_gmapR.o /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
cd gmap/; \
./configure --with-gmapdb= --prefix=/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr \
--libdir=/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/lib
checking package version... 2011-12-28
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
checking target system type... i386-apple-darwin9.8.0
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 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... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
loading script ./config.site
checking bindir... /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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 and cc understand -c and -o together... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -p
checking the name lister (/usr/bin/nm -p) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -p output from gcc object... ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
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... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
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/libexec/gcc/i686-apple-darwin9/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin9.8.0 dyld
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... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
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... 4
checking size of unsigned long long... 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 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... yes
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... yes
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for __builtin_popcount... yes
checking for __builtin_clz... yes
checking for __builtin_ctz... yes
checking for bsr instruction in assembly... yes
checking for popcnt feature... not specified so enabled by default
checking whether -mpopcnt compiler flag works... no
checking gmapdb... /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share
checking MAX_READLENGTH... 200
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... no
checking for samtools library... disabled
checking for goby library... disabled
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 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
Making install in src
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex.o -MD -MP -MF .deps/gmap-oligoindex.Tpo -c -o gmap-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c
mv -f .deps/gmap-oligoindex.Tpo .deps/gmap-oligoindex.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/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
mv -f .deps/gmap-gmap.Tpo .deps/gmap-gmap.Po
/bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read.o gmap-md5.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.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-orderstat.o gmap-oligoindex.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-stage2.o gmap-smooth.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-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lm
libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read.o gmap-md5.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.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-orderstat.o gmap-oligoindex.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-stage2.o gmap-smooth.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-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po
/bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -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-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read.o get_genome-md5.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 -lm
libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -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-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read.o get_genome-md5.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 -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -O3 -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -O3 -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -O3 -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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
mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -O3 -MT gmapindex-iit-write.o -MD -MP -MF .deps/gmapindex-iit-write.Tpo -c -o gmapindex-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c
mv -f .deps/gmapindex-iit-write.Tpo .deps/gmapindex-iit-write.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -O3 -MT gmapindex-indexdb.o -MD -MP -MF .deps/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -O3 -MT gmapindex-table.o -MD -MP -MF .deps/gmapindex-table.Tpo -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c
mv -f .deps/gmapindex-table.Tpo .deps/gmapindex-table.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -O3 -MT gmapindex-tableint.o -MD -MP -MF .deps/gmapindex-tableint.Tpo -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo './'`tableint.c
mv -f .deps/gmapindex-tableint.Tpo .deps/gmapindex-tableint.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -O3 -MT gmapindex-segmentpos.o -MD -MP -MF .deps/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
mv -f .deps/gmapindex-segmentpos.Tpo .deps/gmapindex-segmentpos.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -O3 -MT gmapindex-gmapindex.o -MD -MP -MF .deps/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c
mv -f .deps/gmapindex-gmapindex.Tpo .deps/gmapindex-gmapindex.Po
/bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -O3 -D_THREAD_SAFE -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read.o gmapindex-iit-write.o gmapindex-genomicpos.o gmapindex-compress.o gmapindex-genome-write.o gmapindex-genome_hr.o gmapindex-indexdb.o gmapindex-table.o gmapindex-tableint.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-gmapindex.o -lm
libtool: link: gcc -D_THREAD_SAFE -O3 -D_THREAD_SAFE -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read.o gmapindex-iit-write.o gmapindex-genomicpos.o gmapindex-compress.o gmapindex-genome-write.o gmapindex-genome_hr.o gmapindex-indexdb.o gmapindex-table.o gmapindex-tableint.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-gmapindex.o -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_store-littleendian.Tpo .deps/iit_store-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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
mv -f .deps/iit_store-bigendian.Tpo .deps/iit_store-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_store-access.Tpo .deps/iit_store-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_store-table.Tpo .deps/iit_store-table.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_store-iit_store.Tpo .deps/iit_store-iit_store.Po
/bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -O3 -D_THREAD_SAFE -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-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.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 -D_THREAD_SAFE -O3 -D_THREAD_SAFE -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-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.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
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_get-littleendian.Tpo .deps/iit_get-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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
mv -f .deps/iit_get-bigendian.Tpo .deps/iit_get-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_get-access.Tpo .deps/iit_get-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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
mv -f .deps/iit_get-iit-read.Tpo .deps/iit_get-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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
mv -f .deps/iit_get-parserange.Tpo .deps/iit_get-parserange.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_get-iit_get.Tpo .deps/iit_get-iit_get.Po
/bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -O3 -D_THREAD_SAFE -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-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.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 -D_THREAD_SAFE -O3 -D_THREAD_SAFE -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-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_dump-littleendian.Tpo .deps/iit_dump-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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
mv -f .deps/iit_dump-bigendian.Tpo .deps/iit_dump-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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
mv -f .deps/iit_dump-access.Tpo .deps/iit_dump-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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
mv -f .deps/iit_dump-iit-read.Tpo .deps/iit_dump-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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. -D_THREAD_SAFE -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/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -O3 -D_THREAD_SAFE -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-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm
libtool: link: gcc -D_THREAD_SAFE -O3 -D_THREAD_SAFE -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-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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
mv -f .deps/gsnap-littleendian.Tpo .deps/gsnap-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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
mv -f .deps/gsnap-bigendian.Tpo .deps/gsnap-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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
mv -f .deps/gsnap-access.Tpo .deps/gsnap-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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
mv -f .deps/gsnap-iit-read.Tpo .deps/gsnap-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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
mv -f .deps/gsnap-genome.Tpo .deps/gsnap-genome.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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
mv -f .deps/gsnap-indexdb.Tpo .deps/gsnap-indexdb.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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
mv -f .deps/gsnap-indexdb_hr.Tpo .deps/gsnap-indexdb_hr.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -MT gsnap-oligoindex.o -MD -MP -MF .deps/gsnap-oligoindex.Tpo -c -o gsnap-oligoindex.o `test -f 'oligoindex.c' || echo './'`oligoindex.c
mv -f .deps/gsnap-oligoindex.Tpo .deps/gsnap-oligoindex.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -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/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -D_THREAD_SAFE -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read.o gsnap-md5.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.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.o gsnap-oligoindex_hr.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-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lm
libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=200 -DGSNAP=1 -O3 -D_THREAD_SAFE -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read.o gsnap-md5.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.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.o gsnap-oligoindex_hr.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-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-littleendian.o -MD -MP -MF .deps/snpindex-littleendian.Tpo -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/snpindex-littleendian.Tpo .deps/snpindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-bigendian.o -MD -MP -MF .deps/snpindex-bigendian.Tpo -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/snpindex-bigendian.Tpo .deps/snpindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-access.o -MD -MP -MF .deps/snpindex-access.Tpo -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/snpindex-access.Tpo .deps/snpindex-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/snpindex-iit-read.Tpo .deps/snpindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-indexdb.o -MD -MP -MF .deps/snpindex-indexdb.Tpo -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
mv -f .deps/snpindex-indexdb.Tpo .deps/snpindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-genome.o -MD -MP -MF .deps/snpindex-genome.Tpo -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c
mv -f .deps/snpindex-genome.Tpo .deps/snpindex-genome.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT snpindex-snpindex.o -MD -MP -MF .deps/snpindex-snpindex.Tpo -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c
mv -f .deps/snpindex-snpindex.Tpo .deps/snpindex-snpindex.Po
/bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-genome_hr.o snpindex-indexdb.o snpindex-chrom.o snpindex-md5.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lm
libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-genome_hr.o snpindex-indexdb.o snpindex-chrom.o snpindex-md5.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-littleendian.o -MD -MP -MF .deps/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/cmetindex-littleendian.Tpo .deps/cmetindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-bigendian.o -MD -MP -MF .deps/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/cmetindex-bigendian.Tpo .deps/cmetindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-access.o -MD -MP -MF .deps/cmetindex-access.Tpo -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/cmetindex-access.Tpo .deps/cmetindex-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/cmetindex-iit-read.Tpo .deps/cmetindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT cmetindex-indexdb.o -MD -MP -MF .deps/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
mv -f .deps/cmetindex-indexdb.Tpo .deps/cmetindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -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-interval.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-genome_hr.o cmetindex-indexdb.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm
libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -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-interval.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-genome_hr.o cmetindex-indexdb.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-littleendian.o -MD -MP -MF .deps/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/atoiindex-littleendian.Tpo .deps/atoiindex-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-bigendian.o -MD -MP -MF .deps/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/atoiindex-bigendian.Tpo .deps/atoiindex-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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
mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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. -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -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/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -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-interval.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-genome_hr.o atoiindex-indexdb.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm
libtool: link: gcc -D_THREAD_SAFE -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -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-interval.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-genome_hr.o atoiindex-indexdb.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-except.o -MD -MP -MF .deps/gsnap_tally-except.Tpo -c -o gsnap_tally-except.o `test -f 'except.c' || echo './'`except.c
mv -f .deps/gsnap_tally-except.Tpo .deps/gsnap_tally-except.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-assert.o -MD -MP -MF .deps/gsnap_tally-assert.Tpo -c -o gsnap_tally-assert.o `test -f 'assert.c' || echo './'`assert.c
mv -f .deps/gsnap_tally-assert.Tpo .deps/gsnap_tally-assert.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-mem.o -MD -MP -MF .deps/gsnap_tally-mem.Tpo -c -o gsnap_tally-mem.o `test -f 'mem.c' || echo './'`mem.c
mv -f .deps/gsnap_tally-mem.Tpo .deps/gsnap_tally-mem.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-intlist.o -MD -MP -MF .deps/gsnap_tally-intlist.Tpo -c -o gsnap_tally-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
mv -f .deps/gsnap_tally-intlist.Tpo .deps/gsnap_tally-intlist.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-list.o -MD -MP -MF .deps/gsnap_tally-list.Tpo -c -o gsnap_tally-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/gsnap_tally-list.Tpo .deps/gsnap_tally-list.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-littleendian.o -MD -MP -MF .deps/gsnap_tally-littleendian.Tpo -c -o gsnap_tally-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
mv -f .deps/gsnap_tally-littleendian.Tpo .deps/gsnap_tally-littleendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-bigendian.o -MD -MP -MF .deps/gsnap_tally-bigendian.Tpo -c -o gsnap_tally-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
mv -f .deps/gsnap_tally-bigendian.Tpo .deps/gsnap_tally-bigendian.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-interval.o -MD -MP -MF .deps/gsnap_tally-interval.Tpo -c -o gsnap_tally-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/gsnap_tally-interval.Tpo .deps/gsnap_tally-interval.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-uintlist.o -MD -MP -MF .deps/gsnap_tally-uintlist.Tpo -c -o gsnap_tally-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
mv -f .deps/gsnap_tally-uintlist.Tpo .deps/gsnap_tally-uintlist.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-stopwatch.o -MD -MP -MF .deps/gsnap_tally-stopwatch.Tpo -c -o gsnap_tally-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
mv -f .deps/gsnap_tally-stopwatch.Tpo .deps/gsnap_tally-stopwatch.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-access.o -MD -MP -MF .deps/gsnap_tally-access.Tpo -c -o gsnap_tally-access.o `test -f 'access.c' || echo './'`access.c
mv -f .deps/gsnap_tally-access.Tpo .deps/gsnap_tally-access.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-iit-read.o -MD -MP -MF .deps/gsnap_tally-iit-read.Tpo -c -o gsnap_tally-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
mv -f .deps/gsnap_tally-iit-read.Tpo .deps/gsnap_tally-iit-read.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-chrom.o -MD -MP -MF .deps/gsnap_tally-chrom.Tpo -c -o gsnap_tally-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
mv -f .deps/gsnap_tally-chrom.Tpo .deps/gsnap_tally-chrom.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-genomicpos.o -MD -MP -MF .deps/gsnap_tally-genomicpos.Tpo -c -o gsnap_tally-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
mv -f .deps/gsnap_tally-genomicpos.Tpo .deps/gsnap_tally-genomicpos.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-md5.o -MD -MP -MF .deps/gsnap_tally-md5.Tpo -c -o gsnap_tally-md5.o `test -f 'md5.c' || echo './'`md5.c
mv -f .deps/gsnap_tally-md5.Tpo .deps/gsnap_tally-md5.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-sequence.o -MD -MP -MF .deps/gsnap_tally-sequence.Tpo -c -o gsnap_tally-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
mv -f .deps/gsnap_tally-sequence.Tpo .deps/gsnap_tally-sequence.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-genome.o -MD -MP -MF .deps/gsnap_tally-genome.Tpo -c -o gsnap_tally-genome.o `test -f 'genome.c' || echo './'`genome.c
mv -f .deps/gsnap_tally-genome.Tpo .deps/gsnap_tally-genome.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-gsnapread.o -MD -MP -MF .deps/gsnap_tally-gsnapread.Tpo -c -o gsnap_tally-gsnapread.o `test -f 'gsnapread.c' || echo './'`gsnapread.c
mv -f .deps/gsnap_tally-gsnapread.Tpo .deps/gsnap_tally-gsnapread.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-datadir.o -MD -MP -MF .deps/gsnap_tally-datadir.Tpo -c -o gsnap_tally-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
mv -f .deps/gsnap_tally-datadir.Tpo .deps/gsnap_tally-datadir.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-getopt.o -MD -MP -MF .deps/gsnap_tally-getopt.Tpo -c -o gsnap_tally-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
mv -f .deps/gsnap_tally-getopt.Tpo .deps/gsnap_tally-getopt.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-getopt1.o -MD -MP -MF .deps/gsnap_tally-getopt1.Tpo -c -o gsnap_tally-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
mv -f .deps/gsnap_tally-getopt1.Tpo .deps/gsnap_tally-getopt1.Po
gcc -DHAVE_CONFIG_H -I. -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -MT gsnap_tally-gsnap_tally.o -MD -MP -MF .deps/gsnap_tally-gsnap_tally.Tpo -c -o gsnap_tally-gsnap_tally.o `test -f 'gsnap_tally.c' || echo './'`gsnap_tally.c
mv -f .deps/gsnap_tally-gsnap_tally.Tpo .deps/gsnap_tally-gsnap_tally.Po
/bin/sh ../libtool --tag=CC --mode=link gcc -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -o gsnap_tally gsnap_tally-except.o gsnap_tally-assert.o gsnap_tally-mem.o gsnap_tally-intlist.o gsnap_tally-list.o gsnap_tally-littleendian.o gsnap_tally-bigendian.o gsnap_tally-interval.o gsnap_tally-uintlist.o gsnap_tally-stopwatch.o gsnap_tally-access.o gsnap_tally-iit-read.o gsnap_tally-chrom.o gsnap_tally-genomicpos.o gsnap_tally-md5.o gsnap_tally-sequence.o gsnap_tally-genome.o gsnap_tally-gsnapread.o gsnap_tally-datadir.o gsnap_tally-getopt.o gsnap_tally-getopt1.o gsnap_tally-gsnap_tally.o -lz -lm
libtool: link: gcc -D_THREAD_SAFE -DTARGET=\"i386-apple-darwin9.8.0\" -DGMAPDB=\"/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share\" -O3 -D_THREAD_SAFE -o gsnap_tally gsnap_tally-except.o gsnap_tally-assert.o gsnap_tally-mem.o gsnap_tally-intlist.o gsnap_tally-list.o gsnap_tally-littleendian.o gsnap_tally-bigendian.o gsnap_tally-interval.o gsnap_tally-uintlist.o gsnap_tally-stopwatch.o gsnap_tally-access.o gsnap_tally-iit-read.o gsnap_tally-chrom.o gsnap_tally-genomicpos.o gsnap_tally-md5.o gsnap_tally-sequence.o gsnap_tally-genome.o gsnap_tally-gsnapread.o gsnap_tally-datadir.o gsnap_tally-getopt.o gsnap_tally-getopt1.o gsnap_tally-gsnap_tally.o -lz -lm
test -z "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin" || ../config/install-sh -c -d "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin"
/bin/sh ../libtool --mode=install /usr/bin/install -c 'gmap' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap'
libtool: install: /usr/bin/install -c gmap /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap
/bin/sh ../libtool --mode=install /usr/bin/install -c 'get-genome' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/get-genome'
libtool: install: /usr/bin/install -c get-genome /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/get-genome
/bin/sh ../libtool --mode=install /usr/bin/install -c 'gmapindex' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmapindex'
libtool: install: /usr/bin/install -c gmapindex /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmapindex
/bin/sh ../libtool --mode=install /usr/bin/install -c 'iit_store' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_store'
libtool: install: /usr/bin/install -c iit_store /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_store
/bin/sh ../libtool --mode=install /usr/bin/install -c 'iit_get' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_get'
libtool: install: /usr/bin/install -c iit_get /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_get
/bin/sh ../libtool --mode=install /usr/bin/install -c 'iit_dump' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_dump'
libtool: install: /usr/bin/install -c iit_dump /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/iit_dump
/bin/sh ../libtool --mode=install /usr/bin/install -c 'gsnap' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gsnap'
libtool: install: /usr/bin/install -c gsnap /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gsnap
/bin/sh ../libtool --mode=install /usr/bin/install -c 'snpindex' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/snpindex'
libtool: install: /usr/bin/install -c snpindex /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/snpindex
/bin/sh ../libtool --mode=install /usr/bin/install -c 'cmetindex' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/cmetindex'
libtool: install: /usr/bin/install -c cmetindex /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/cmetindex
/bin/sh ../libtool --mode=install /usr/bin/install -c 'atoiindex' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/atoiindex'
libtool: install: /usr/bin/install -c atoiindex /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/atoiindex
/bin/sh ../libtool --mode=install /usr/bin/install -c 'gsnap_tally' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gsnap_tally'
libtool: install: /usr/bin/install -c gsnap_tally /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gsnap_tally
make[3]: Nothing to be done for `install-data-am'.
Making install in 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
test -z "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin" || ../config/install-sh -c -d "/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin"
/usr/bin/install -c 'gmap_compress' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_compress'
/usr/bin/install -c 'gmap_uncompress' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_uncompress'
/usr/bin/install -c 'gmap_process' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_process'
/usr/bin/install -c 'gmap_setup' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_setup'
/usr/bin/install -c 'gmap_build' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_build'
/usr/bin/install -c 'gmap_reassemble' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gmap_reassemble'
/usr/bin/install -c 'md_coords' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/md_coords'
/usr/bin/install -c 'fa_coords' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/fa_coords'
/usr/bin/install -c 'psl_splicesites' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/psl_splicesites'
/usr/bin/install -c 'psl_introns' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/psl_introns'
/usr/bin/install -c 'psl_genes' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/psl_genes'
/usr/bin/install -c 'gtf_splicesites' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gtf_splicesites'
/usr/bin/install -c 'gtf_introns' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gtf_introns'
/usr/bin/install -c 'gtf_genes' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gtf_genes'
/usr/bin/install -c 'gff3_splicesites' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gff3_splicesites'
/usr/bin/install -c 'gff3_introns' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gff3_introns'
/usr/bin/install -c 'gff3_genes' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/gff3_genes'
/usr/bin/install -c 'dbsnp_iit' '/Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/bin/dbsnp_iit'
make[3]: Nothing to be done for `install-data-am'.
Making install in tests
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Nothing to be done for `install-exec-am'.
/bin/sh /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/gmap/config/install-sh -d /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/00_pkg_src/gmapR/src/../inst/usr/share
installing to /Users/biocbuild/bbs-2.12-bioc/meat/gmapR.Rcheck/gmapR/libs/i386
** R
** inst
** preparing 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'
** help
*** installing help indices
** building package indices
** installing vignettes
'gmapR.Rnw'
** testing if installed package can be loaded
* DONE (gmapR)