############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL gmapR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘gmapR’ ... ** using staged installation ** libs cd gstruct/; \ CFLAGS="-g -O3" \ ./configure --enable-static --disable-shared \ --prefix=/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr --includedir=/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include/gstruct \ --libdir=/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib \ --with-samtools-lib=/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/samtools \ --disable-maintainer-mode \ --disable-binaries checking package version... 2017-01-01 checking whether to enable maintainer-specific portions of Makefiles... no loading default site script ./config.site checking CFLAGS... -g -O3 checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking target system type... aarch64-unknown-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking bindir... /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin checking whether to link statically... not specified so disabled by default checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /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/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for qsub... no checking gmap program directory... checking for get-genome... false checking for iit_store... false checking for iit_get... false checking for gmap_build... false checking for gmap... false checking for gsnap... false checking for sam_sort... false checking for uniqscan... false checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for builtin popcount/clz/ctz features... not specified so enabled by default ./configure: line 16919: ACX_BUILTIN_POPCOUNT: command not found checking for bsr instruction in assembly... yes checking whether sse2 is enabled... not specified so enabled by default checking compiler is defective and requires an immediate in sse2 shift commands... yes checking whether ssse3 is enabled... not specified so enabled by default checking whether sse4.1 is enabled... not specified so enabled by default checking whether sse4.2 is enabled... not specified so enabled by default checking whether avx is enabled... not specified so enabled by default checking whether avx2 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking gmapdb... /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share checking whether to make binaries... disabled checking for zlib support... enabled checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for samtools program... checking for samtools library... provided by --with-samtools-lib checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating lib/gstruct-1.0.pc config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: WARNING: You don't seem to have gsnap specified. checking Standard compiler and flags to be used... gcc -g -O3 checking Standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt compiler flags to be used... checking SIMD features available on computer... checking SIMD compiler flags to be used... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bgzf.c -o samtools/bgzf.o samtools/bgzf.c: In function ‘worker_aux’: samtools/bgzf.c:412:16: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 412 | int i, tmp, stop = 0; | ^~~ samtools/bgzf.c: In function ‘bgzf_close’: samtools/bgzf.c:592:18: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 592 | int ret, count, block_length; | ^~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kstring.c -o samtools/kstring.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_aux.c -o samtools/bam_aux.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam.c -o samtools/bam.o samtools/bam.c: In function ‘bam_header_write’: samtools/bam.c:128:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 128 | strncpy(buf, "BAM\001", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_import.c -o samtools/bam_import.o In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/limits.h:26, from /opt/ohpc/pub/compiler/gcc/14.2.0/lib/gcc/aarch64-unknown-linux-gnu/14.2.0/include/limits.h:210, from /opt/ohpc/pub/compiler/gcc/14.2.0/lib/gcc/aarch64-unknown-linux-gnu/14.2.0/include/syslimits.h:7, from /opt/ohpc/pub/compiler/gcc/14.2.0/lib/gcc/aarch64-unknown-linux-gnu/14.2.0/include/limits.h:34, from /usr/include/zconf.h:424, from /usr/include/zlib.h:34, from samtools/bam_import.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam.c -o samtools/sam.o In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/string.h:26, from samtools/sam.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_index.c -o samtools/bam_index.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_pileup.c -o samtools/bam_pileup.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_md.c -o samtools/bam_md.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/razf.c -o samtools/razf.o samtools/razf.c: In function ‘razf_open_w’: samtools/razf.c:178:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 178 | strncpy((char*)rz->header->extra, "RAZF", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/faidx.c -o samtools/faidx.o samtools/faidx.c: In function ‘fai_load0’: samtools/faidx.c:309:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 309 | else | ^~~~ samtools/faidx.c:312:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 312 | if (fp == 0) { | ^~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/knetfile.c -o samtools/knetfile.o In file included from /usr/include/time.h:25, from samtools/knetfile.c:33: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_sort.c -o samtools/bam_sort.o In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdlib.h:26, from samtools/bam_sort.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/sam_header.c -o samtools/sam_header.o In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/sam_header.c:3: /usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/bam_reheader.c -o samtools/bam_reheader.o samtools/bam_reheader.c: In function ‘bam_reheader’: samtools/bam_reheader.c:12:23: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] 12 | bam_header_t *old; | ^~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/kprobaln.c -o samtools/kprobaln.o samtools/kprobaln.c: In function ‘kpa_glocal’: samtools/kprobaln.c:78:28: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] 78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | ^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -c samtools/samtools_patch.c -o samtools/samtools_patch.o ar -crus samtools/libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/samtools_patch.o cd gstruct; \ make install make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct' Making install in src make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c -o libgstruct_1.0_la-except.lo `test -f 'except.c' || echo './'`except.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-except.lo -MD -MP -MF .deps/libgstruct_1.0_la-except.Tpo -c except.c -o libgstruct_1.0_la-except.o mv -f .deps/libgstruct_1.0_la-except.Tpo .deps/libgstruct_1.0_la-except.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c -o libgstruct_1.0_la-assert.lo `test -f 'assert.c' || echo './'`assert.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-assert.lo -MD -MP -MF .deps/libgstruct_1.0_la-assert.Tpo -c assert.c -o libgstruct_1.0_la-assert.o mv -f .deps/libgstruct_1.0_la-assert.Tpo .deps/libgstruct_1.0_la-assert.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c -o libgstruct_1.0_la-mem.lo `test -f 'mem.c' || echo './'`mem.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mem.lo -MD -MP -MF .deps/libgstruct_1.0_la-mem.Tpo -c mem.c -o libgstruct_1.0_la-mem.o mv -f .deps/libgstruct_1.0_la-mem.Tpo .deps/libgstruct_1.0_la-mem.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c -o libgstruct_1.0_la-intlist.lo `test -f 'intlist.c' || echo './'`intlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-intlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-intlist.Tpo -c intlist.c -o libgstruct_1.0_la-intlist.o mv -f .deps/libgstruct_1.0_la-intlist.Tpo .deps/libgstruct_1.0_la-intlist.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c -o libgstruct_1.0_la-list.lo `test -f 'list.c' || echo './'`list.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-list.lo -MD -MP -MF .deps/libgstruct_1.0_la-list.Tpo -c list.c -o libgstruct_1.0_la-list.o mv -f .deps/libgstruct_1.0_la-list.Tpo .deps/libgstruct_1.0_la-list.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c -o libgstruct_1.0_la-littleendian.lo `test -f 'littleendian.c' || echo './'`littleendian.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-littleendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-littleendian.Tpo -c littleendian.c -o libgstruct_1.0_la-littleendian.o 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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c -o libgstruct_1.0_la-bigendian.lo `test -f 'bigendian.c' || echo './'`bigendian.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bigendian.lo -MD -MP -MF .deps/libgstruct_1.0_la-bigendian.Tpo -c bigendian.c -o libgstruct_1.0_la-bigendian.o 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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c -o libgstruct_1.0_la-interval.lo `test -f 'interval.c' || echo './'`interval.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-interval.lo -MD -MP -MF .deps/libgstruct_1.0_la-interval.Tpo -c interval.c -o libgstruct_1.0_la-interval.o mv -f .deps/libgstruct_1.0_la-interval.Tpo .deps/libgstruct_1.0_la-interval.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c -o libgstruct_1.0_la-uintlist.lo `test -f 'uintlist.c' || echo './'`uintlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uintlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-uintlist.Tpo -c uintlist.c -o libgstruct_1.0_la-uintlist.o mv -f .deps/libgstruct_1.0_la-uintlist.Tpo .deps/libgstruct_1.0_la-uintlist.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c -o libgstruct_1.0_la-stopwatch.lo `test -f 'stopwatch.c' || echo './'`stopwatch.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-stopwatch.lo -MD -MP -MF .deps/libgstruct_1.0_la-stopwatch.Tpo -c stopwatch.c -o libgstruct_1.0_la-stopwatch.o mv -f .deps/libgstruct_1.0_la-stopwatch.Tpo .deps/libgstruct_1.0_la-stopwatch.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c -o libgstruct_1.0_la-access.lo `test -f 'access.c' || echo './'`access.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-access.lo -MD -MP -MF .deps/libgstruct_1.0_la-access.Tpo -c access.c -o libgstruct_1.0_la-access.o access.c: In function ‘Access_file_exists_p’: access.c:59:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 59 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat 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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c -o libgstruct_1.0_la-iit-read.lo `test -f 'iit-read.c' || echo './'`iit-read.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-read.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-read.Tpo -c iit-read.c -o libgstruct_1.0_la-iit-read.o 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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c -o libgstruct_1.0_la-chrom.lo `test -f 'chrom.c' || echo './'`chrom.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrom.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrom.Tpo -c chrom.c -o libgstruct_1.0_la-chrom.o chrom.c: In function ‘Chrom_from_string’: chrom.c:108:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 108 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:108:10: note: did you mean to dereference the pointer? 108 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ 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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c -o libgstruct_1.0_la-genomicpos.lo `test -f 'genomicpos.c' || echo './'`genomicpos.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genomicpos.lo -MD -MP -MF .deps/libgstruct_1.0_la-genomicpos.Tpo -c genomicpos.c -o libgstruct_1.0_la-genomicpos.o mv -f .deps/libgstruct_1.0_la-genomicpos.Tpo .deps/libgstruct_1.0_la-genomicpos.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c -o libgstruct_1.0_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-md5.lo -MD -MP -MF .deps/libgstruct_1.0_la-md5.Tpo -c md5.c -o libgstruct_1.0_la-md5.o In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ 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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c -o libgstruct_1.0_la-sequence.lo `test -f 'sequence.c' || echo './'`sequence.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-sequence.lo -MD -MP -MF .deps/libgstruct_1.0_la-sequence.Tpo -c sequence.c -o libgstruct_1.0_la-sequence.o mv -f .deps/libgstruct_1.0_la-sequence.Tpo .deps/libgstruct_1.0_la-sequence.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c -o libgstruct_1.0_la-genome.lo `test -f 'genome.c' || echo './'`genome.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-genome.lo -MD -MP -MF .deps/libgstruct_1.0_la-genome.Tpo -c genome.c -o libgstruct_1.0_la-genome.o 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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c -o libgstruct_1.0_la-uinttable.lo `test -f 'uinttable.c' || echo './'`uinttable.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-uinttable.lo -MD -MP -MF .deps/libgstruct_1.0_la-uinttable.Tpo -c uinttable.c -o libgstruct_1.0_la-uinttable.o mv -f .deps/libgstruct_1.0_la-uinttable.Tpo .deps/libgstruct_1.0_la-uinttable.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c -o libgstruct_1.0_la-table.lo `test -f 'table.c' || echo './'`table.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-table.lo -MD -MP -MF .deps/libgstruct_1.0_la-table.Tpo -c table.c -o libgstruct_1.0_la-table.o mv -f .deps/libgstruct_1.0_la-table.Tpo .deps/libgstruct_1.0_la-table.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c -o libgstruct_1.0_la-chrnum.lo `test -f 'chrnum.c' || echo './'`chrnum.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-chrnum.lo -MD -MP -MF .deps/libgstruct_1.0_la-chrnum.Tpo -c chrnum.c -o libgstruct_1.0_la-chrnum.o mv -f .deps/libgstruct_1.0_la-chrnum.Tpo .deps/libgstruct_1.0_la-chrnum.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c -o libgstruct_1.0_la-bamread.lo `test -f 'bamread.c' || echo './'`bamread.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamread.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamread.Tpo -c bamread.c -o libgstruct_1.0_la-bamread.o mv -f .deps/libgstruct_1.0_la-bamread.Tpo .deps/libgstruct_1.0_la-bamread.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c -o libgstruct_1.0_la-samread.lo `test -f 'samread.c' || echo './'`samread.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-samread.lo -MD -MP -MF .deps/libgstruct_1.0_la-samread.Tpo -c samread.c -o libgstruct_1.0_la-samread.o mv -f .deps/libgstruct_1.0_la-samread.Tpo .deps/libgstruct_1.0_la-samread.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c -o libgstruct_1.0_la-parserange.lo `test -f 'parserange.c' || echo './'`parserange.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-parserange.lo -MD -MP -MF .deps/libgstruct_1.0_la-parserange.Tpo -c parserange.c -o libgstruct_1.0_la-parserange.o mv -f .deps/libgstruct_1.0_la-parserange.Tpo .deps/libgstruct_1.0_la-parserange.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c -o libgstruct_1.0_la-tableuint.lo `test -f 'tableuint.c' || echo './'`tableuint.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tableuint.lo -MD -MP -MF .deps/libgstruct_1.0_la-tableuint.Tpo -c tableuint.c -o libgstruct_1.0_la-tableuint.o mv -f .deps/libgstruct_1.0_la-tableuint.Tpo .deps/libgstruct_1.0_la-tableuint.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c -o libgstruct_1.0_la-iit-write.lo `test -f 'iit-write.c' || echo './'`iit-write.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-iit-write.lo -MD -MP -MF .deps/libgstruct_1.0_la-iit-write.Tpo -c iit-write.c -o libgstruct_1.0_la-iit-write.o mv -f .deps/libgstruct_1.0_la-iit-write.Tpo .deps/libgstruct_1.0_la-iit-write.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c -o libgstruct_1.0_la-ucharlist.lo `test -f 'ucharlist.c' || echo './'`ucharlist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-ucharlist.lo -MD -MP -MF .deps/libgstruct_1.0_la-ucharlist.Tpo -c ucharlist.c -o libgstruct_1.0_la-ucharlist.o mv -f .deps/libgstruct_1.0_la-ucharlist.Tpo .deps/libgstruct_1.0_la-ucharlist.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c -o libgstruct_1.0_la-matchpool.lo `test -f 'matchpool.c' || echo './'`matchpool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-matchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-matchpool.Tpo -c matchpool.c -o libgstruct_1.0_la-matchpool.o mv -f .deps/libgstruct_1.0_la-matchpool.Tpo .deps/libgstruct_1.0_la-matchpool.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c -o libgstruct_1.0_la-mismatchpool.lo `test -f 'mismatchpool.c' || echo './'`mismatchpool.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-mismatchpool.lo -MD -MP -MF .deps/libgstruct_1.0_la-mismatchpool.Tpo -c mismatchpool.c -o libgstruct_1.0_la-mismatchpool.o mv -f .deps/libgstruct_1.0_la-mismatchpool.Tpo .deps/libgstruct_1.0_la-mismatchpool.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c -o libgstruct_1.0_la-tally.lo `test -f 'tally.c' || echo './'`tally.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-tally.lo -MD -MP -MF .deps/libgstruct_1.0_la-tally.Tpo -c tally.c -o libgstruct_1.0_la-tally.o mv -f .deps/libgstruct_1.0_la-tally.Tpo .deps/libgstruct_1.0_la-tally.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c -o libgstruct_1.0_la-translation.lo `test -f 'translation.c' || echo './'`translation.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-translation.lo -MD -MP -MF .deps/libgstruct_1.0_la-translation.Tpo -c translation.c -o libgstruct_1.0_la-translation.o mv -f .deps/libgstruct_1.0_la-translation.Tpo .deps/libgstruct_1.0_la-translation.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c -o libgstruct_1.0_la-expr.lo `test -f 'expr.c' || echo './'`expr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-expr.lo -MD -MP -MF .deps/libgstruct_1.0_la-expr.Tpo -c expr.c -o libgstruct_1.0_la-expr.o mv -f .deps/libgstruct_1.0_la-expr.Tpo .deps/libgstruct_1.0_la-expr.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c -o libgstruct_1.0_la-bamtally.lo `test -f 'bamtally.c' || echo './'`bamtally.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-bamtally.lo -MD -MP -MF .deps/libgstruct_1.0_la-bamtally.Tpo -c bamtally.c -o libgstruct_1.0_la-bamtally.o 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. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c -o libgstruct_1.0_la-datadir.lo `test -f 'datadir.c' || echo './'`datadir.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -MT libgstruct_1.0_la-datadir.lo -MD -MP -MF .deps/libgstruct_1.0_la-datadir.Tpo -c datadir.c -o libgstruct_1.0_la-datadir.o mv -f .deps/libgstruct_1.0_la-datadir.Tpo .deps/libgstruct_1.0_la-datadir.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -I. -fPIC -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -g -O3 -version-info 1:0:0 -o libgstruct-1.0.la -rpath /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib libgstruct_1.0_la-except.lo libgstruct_1.0_la-assert.lo libgstruct_1.0_la-mem.lo libgstruct_1.0_la-intlist.lo libgstruct_1.0_la-list.lo libgstruct_1.0_la-littleendian.lo libgstruct_1.0_la-bigendian.lo libgstruct_1.0_la-interval.lo libgstruct_1.0_la-uintlist.lo libgstruct_1.0_la-stopwatch.lo libgstruct_1.0_la-access.lo libgstruct_1.0_la-iit-read.lo libgstruct_1.0_la-chrom.lo libgstruct_1.0_la-genomicpos.lo libgstruct_1.0_la-md5.lo libgstruct_1.0_la-sequence.lo libgstruct_1.0_la-genome.lo libgstruct_1.0_la-uinttable.lo libgstruct_1.0_la-table.lo libgstruct_1.0_la-chrnum.lo libgstruct_1.0_la-bamread.lo libgstruct_1.0_la-samread.lo libgstruct_1.0_la-parserange.lo libgstruct_1.0_la-tableuint.lo libgstruct_1.0_la-iit-write.lo libgstruct_1.0_la-ucharlist.lo libgstruct_1.0_la-matchpool.lo libgstruct_1.0_la-mismatchpool.lo libgstruct_1.0_la-tally.lo libgstruct_1.0_la-translation.lo libgstruct_1.0_la-expr.lo libgstruct_1.0_la-bamtally.lo libgstruct_1.0_la-datadir.lo -lz -lm libtool: link: ar cru .libs/libgstruct-1.0.a libgstruct_1.0_la-except.o libgstruct_1.0_la-assert.o libgstruct_1.0_la-mem.o libgstruct_1.0_la-intlist.o libgstruct_1.0_la-list.o libgstruct_1.0_la-littleendian.o libgstruct_1.0_la-bigendian.o libgstruct_1.0_la-interval.o libgstruct_1.0_la-uintlist.o libgstruct_1.0_la-stopwatch.o libgstruct_1.0_la-access.o libgstruct_1.0_la-iit-read.o libgstruct_1.0_la-chrom.o libgstruct_1.0_la-genomicpos.o libgstruct_1.0_la-md5.o libgstruct_1.0_la-sequence.o libgstruct_1.0_la-genome.o libgstruct_1.0_la-uinttable.o libgstruct_1.0_la-table.o libgstruct_1.0_la-chrnum.o libgstruct_1.0_la-bamread.o libgstruct_1.0_la-samread.o libgstruct_1.0_la-parserange.o libgstruct_1.0_la-tableuint.o libgstruct_1.0_la-iit-write.o libgstruct_1.0_la-ucharlist.o libgstruct_1.0_la-matchpool.o libgstruct_1.0_la-mismatchpool.o libgstruct_1.0_la-tally.o libgstruct_1.0_la-translation.o libgstruct_1.0_la-expr.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" ) make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct/src' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libgstruct-1.0.la '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib' libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.lai /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.la libtool: install: /usr/bin/install -c .libs/libgstruct-1.0.a /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: chmod 644 /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: install: ranlib /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a libtool: finish: PATH="/home/biocbuild/.cargo/bin:/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/opt/meme/bin:/opt/meme/libexec/meme-5.5.5:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include/gstruct' /usr/bin/install -c -m 644 config.h fopen.h bool.h types.h except.h assert.h mem.h intlistdef.h intlist.h listdef.h list.h littleendian.h bigendian.h interval.h uintlist.h stopwatch.h access.h iitdef.h iit-read.h chrom.h genomicpos.h md5.h complement.h sequence.h genome.h uinttable.h table.h chrnum.h bamread.h samread.h parserange.h dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h tableuint.h iit-write.h ucharlist.h matchdef.h '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include/gstruct' /usr/bin/install -c -m 644 matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include/gstruct' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig' /usr/bin/install -c -m 644 ../lib/gstruct-1.0.pc '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib/pkgconfig' make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct/src' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct/src' make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct' make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gstruct' /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bamreader.c -o bamreader.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bamtally.c -o bamtally.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c iit.c -o iit.o In function ‘_convert_matches’, inlined from ‘R_iit_read’ at iit.c:290:12: iit.c:267:39: warning: ‘fields’ may be used uninitialized [-Wmaybe-uninitialized] 267 | mkChar(IIT_fieldvalue(iit, i, fields[f]))); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit.c: In function ‘R_iit_read’: iit.c:214:10: note: ‘fields’ was declared here 214 | int *fields; | ^~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c variantsummary.c -o variantsummary.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c genome.c -o genome.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/include -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c R_init_gmapR.c -o R_init_gmapR.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L"/home/biocbuild/R/R/lib" -L/usr/local/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz -L"/home/biocbuild/R/R/lib" -lR cd gmap/; \ ./configure --with-gmapdb= --prefix=/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr \ --libdir=/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/lib --disable-maintainer-mode checking package version... 2013-11-01 checking whether to enable maintainer-specific portions of Makefiles... no checking CONFIG_SITE... ./config.site loading script ./config.site checking CFLAGS... not set by user so using default -O3 checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking target system type... aarch64-unknown-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking bindir... /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /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/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for _LARGEFILE_SOURCE value needed for large files... no checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for popcnt feature... not specified so enabled by default checking for __builtin_popcount... yes checking for __builtin_clz... yes checking for __builtin_ctz... yes checking for bsr instruction in assembly... yes checking whether sse2 is enabled... not specified so enabled by default checking whether user has declared a defective SSE2 compiler... no checking whether sse4.1 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking gmapdb... /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share checking MAX_READLENGTH... 250 checking for zlib support... enabled checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking for goby library... disabled checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_compress.pl config.status: creating util/gmap_uncompress.pl config.status: creating util/gmap_process.pl config.status: creating util/gmap_setup.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_reassemble.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands cd gmap; \ make install make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap' Making install in src make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/src' gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-except.o -MD -MP -MF .deps/gmap-except.Tpo -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmap-except.Tpo .deps/gmap-except.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-assert.o -MD -MP -MF .deps/gmap-assert.Tpo -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmap-assert.Tpo .deps/gmap-assert.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-mem.o -MD -MP -MF .deps/gmap-mem.Tpo -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmap-mem.Tpo .deps/gmap-mem.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intlist.o -MD -MP -MF .deps/gmap-intlist.Tpo -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmap-intlist.Tpo .deps/gmap-intlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-list.o -MD -MP -MF .deps/gmap-list.Tpo -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmap-list.Tpo .deps/gmap-list.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-littleendian.o -MD -MP -MF .deps/gmap-littleendian.Tpo -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gmap-littleendian.Tpo .deps/gmap-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bigendian.o -MD -MP -MF .deps/gmap-bigendian.Tpo -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gmap-bigendian.Tpo .deps/gmap-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-univinterval.o -MD -MP -MF .deps/gmap-univinterval.Tpo -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/gmap-univinterval.Tpo .deps/gmap-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-interval.o -MD -MP -MF .deps/gmap-interval.Tpo -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmap-interval.Tpo .deps/gmap-interval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uintlist.o -MD -MP -MF .deps/gmap-uintlist.Tpo -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmap-uintlist.Tpo .deps/gmap-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stopwatch.o -MD -MP -MF .deps/gmap-stopwatch.Tpo -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmap-stopwatch.Tpo .deps/gmap-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-access.o -MD -MP -MF .deps/gmap-access.Tpo -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/gmap-access.Tpo .deps/gmap-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read-univ.o -MD -MP -MF .deps/gmap-iit-read-univ.Tpo -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/gmap-iit-read-univ.Tpo .deps/gmap-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-iit-read.o -MD -MP -MF .deps/gmap-iit-read.Tpo -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gmap-iit-read.Tpo .deps/gmap-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-md5.o -MD -MP -MF .deps/gmap-md5.Tpo -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/gmap-md5.Tpo .deps/gmap-md5.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bzip2.o -MD -MP -MF .deps/gmap-bzip2.Tpo -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmap-bzip2.Tpo .deps/gmap-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-sequence.o -MD -MP -MF .deps/gmap-sequence.Tpo -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmap-sequence.Tpo .deps/gmap-sequence.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-reader.o -MD -MP -MF .deps/gmap-reader.Tpo -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gmap-reader.Tpo .deps/gmap-reader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genomicpos.o -MD -MP -MF .deps/gmap-genomicpos.Tpo -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmap-genomicpos.Tpo .deps/gmap-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress.o -MD -MP -MF .deps/gmap-compress.Tpo -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmap-compress.Tpo .deps/gmap-compress.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-compress-write.o -MD -MP -MF .deps/gmap-compress-write.Tpo -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c mv -f .deps/gmap-compress-write.Tpo .deps/gmap-compress-write.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gbuffer.o -MD -MP -MF .deps/gmap-gbuffer.Tpo -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gmap-gbuffer.Tpo .deps/gmap-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome.o -MD -MP -MF .deps/gmap-genome.Tpo -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/gmap-genome.Tpo .deps/gmap-genome.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_hr.o -MD -MP -MF .deps/gmap-genome_hr.Tpo -c -o gmap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmap-genome_hr.Tpo .deps/gmap-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome_sites.o -MD -MP -MF .deps/gmap-genome_sites.Tpo -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gmap-genome_sites.Tpo .deps/gmap-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-genome-write.o -MD -MP -MF .deps/gmap-genome-write.Tpo -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c mv -f .deps/gmap-genome-write.Tpo .deps/gmap-genome-write.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-bitpack64-read.o -MD -MP -MF .deps/gmap-bitpack64-read.Tpo -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmap-bitpack64-read.Tpo .deps/gmap-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb.o -MD -MP -MF .deps/gmap-indexdb.Tpo -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/gmap-indexdb.Tpo .deps/gmap-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-indexdb_hr.o -MD -MP -MF .deps/gmap-indexdb_hr.Tpo -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/gmap-indexdb_hr.Tpo .deps/gmap-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligo.o -MD -MP -MF .deps/gmap-oligo.Tpo -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gmap-oligo.Tpo .deps/gmap-oligo.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-block.o -MD -MP -MF .deps/gmap-block.Tpo -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c mv -f .deps/gmap-block.Tpo .deps/gmap-block.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrom.o -MD -MP -MF .deps/gmap-chrom.Tpo -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gmap-chrom.Tpo .deps/gmap-chrom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-segmentpos.o -MD -MP -MF .deps/gmap-segmentpos.Tpo -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gmap-segmentpos.Tpo .deps/gmap-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrnum.o -MD -MP -MF .deps/gmap-chrnum.Tpo -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gmap-chrnum.Tpo .deps/gmap-chrnum.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chrsubset.o -MD -MP -MF .deps/gmap-chrsubset.Tpo -c -o gmap-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/gmap-chrsubset.Tpo .deps/gmap-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-uinttable.o -MD -MP -MF .deps/gmap-uinttable.Tpo -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c mv -f .deps/gmap-uinttable.Tpo .deps/gmap-uinttable.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gregion.o -MD -MP -MF .deps/gmap-gregion.Tpo -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c mv -f .deps/gmap-gregion.Tpo .deps/gmap-gregion.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-match.o -MD -MP -MF .deps/gmap-match.Tpo -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c mv -f .deps/gmap-match.Tpo .deps/gmap-match.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-matchpool.o -MD -MP -MF .deps/gmap-matchpool.Tpo -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c mv -f .deps/gmap-matchpool.Tpo .deps/gmap-matchpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagnostic.o -MD -MP -MF .deps/gmap-diagnostic.Tpo -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c mv -f .deps/gmap-diagnostic.Tpo .deps/gmap-diagnostic.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage1.o -MD -MP -MF .deps/gmap-stage1.Tpo -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c mv -f .deps/gmap-stage1.Tpo .deps/gmap-stage1.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diag.o -MD -MP -MF .deps/gmap-diag.Tpo -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gmap-diag.Tpo .deps/gmap-diag.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-diagpool.o -MD -MP -MF .deps/gmap-diagpool.Tpo -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gmap-diagpool.Tpo .deps/gmap-diagpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cmet.o -MD -MP -MF .deps/gmap-cmet.Tpo -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gmap-cmet.Tpo .deps/gmap-cmet.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-atoi.o -MD -MP -MF .deps/gmap-atoi.Tpo -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gmap-atoi.Tpo .deps/gmap-atoi.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-orderstat.o -MD -MP -MF .deps/gmap-orderstat.Tpo -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gmap-orderstat.Tpo .deps/gmap-orderstat.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-oligoindex_hr.o -MD -MP -MF .deps/gmap-oligoindex_hr.Tpo -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gmap-oligoindex_hr.Tpo .deps/gmap-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-intron.o -MD -MP -MF .deps/gmap-intron.Tpo -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gmap-intron.Tpo .deps/gmap-intron.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent.o -MD -MP -MF .deps/gmap-maxent.Tpo -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gmap-maxent.Tpo .deps/gmap-maxent.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-maxent_hr.o -MD -MP -MF .deps/gmap-maxent_hr.Tpo -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gmap-maxent_hr.Tpo .deps/gmap-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pair.o -MD -MP -MF .deps/gmap-pair.Tpo -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c mv -f .deps/gmap-pair.Tpo .deps/gmap-pair.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pairpool.o -MD -MP -MF .deps/gmap-pairpool.Tpo -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gmap-pairpool.Tpo .deps/gmap-pairpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-cellpool.o -MD -MP -MF .deps/gmap-cellpool.Tpo -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gmap-cellpool.Tpo .deps/gmap-cellpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage2.o -MD -MP -MF .deps/gmap-stage2.Tpo -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gmap-stage2.Tpo .deps/gmap-stage2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-doublelist.o -MD -MP -MF .deps/gmap-doublelist.Tpo -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gmap-doublelist.Tpo .deps/gmap-doublelist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-smooth.o -MD -MP -MF .deps/gmap-smooth.Tpo -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gmap-smooth.Tpo .deps/gmap-smooth.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicestringpool.o -MD -MP -MF .deps/gmap-splicestringpool.Tpo -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gmap-splicestringpool.Tpo .deps/gmap-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie_build.o -MD -MP -MF .deps/gmap-splicetrie_build.Tpo -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gmap-splicetrie_build.Tpo .deps/gmap-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-splicetrie.o -MD -MP -MF .deps/gmap-splicetrie.Tpo -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gmap-splicetrie.Tpo .deps/gmap-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-boyer-moore.o -MD -MP -MF .deps/gmap-boyer-moore.Tpo -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gmap-boyer-moore.Tpo .deps/gmap-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-dynprog.o -MD -MP -MF .deps/gmap-dynprog.Tpo -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gmap-dynprog.Tpo .deps/gmap-dynprog.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-translation.o -MD -MP -MF .deps/gmap-translation.Tpo -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gmap-translation.Tpo .deps/gmap-translation.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-pbinom.o -MD -MP -MF .deps/gmap-pbinom.Tpo -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gmap-pbinom.Tpo .deps/gmap-pbinom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-changepoint.o -MD -MP -MF .deps/gmap-changepoint.Tpo -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gmap-changepoint.Tpo .deps/gmap-changepoint.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-stage3.o -MD -MP -MF .deps/gmap-stage3.Tpo -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gmap-stage3.Tpo .deps/gmap-stage3.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-request.o -MD -MP -MF .deps/gmap-request.Tpo -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gmap-request.Tpo .deps/gmap-request.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-result.o -MD -MP -MF .deps/gmap-result.Tpo -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c mv -f .deps/gmap-result.Tpo .deps/gmap-result.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-inbuffer.o -MD -MP -MF .deps/gmap-inbuffer.Tpo -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gmap-inbuffer.Tpo .deps/gmap-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-samheader.o -MD -MP -MF .deps/gmap-samheader.Tpo -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gmap-samheader.Tpo .deps/gmap-samheader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-outbuffer.o -MD -MP -MF .deps/gmap-outbuffer.Tpo -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gmap-outbuffer.Tpo .deps/gmap-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-chimera.o -MD -MP -MF .deps/gmap-chimera.Tpo -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gmap-chimera.Tpo .deps/gmap-chimera.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-datadir.o -MD -MP -MF .deps/gmap-datadir.Tpo -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gmap-datadir.Tpo .deps/gmap-datadir.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt.o -MD -MP -MF .deps/gmap-getopt.Tpo -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gmap-getopt.Tpo .deps/gmap-getopt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-getopt1.o -MD -MP -MF .deps/gmap-getopt1.Tpo -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gmap-getopt1.Tpo .deps/gmap-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -MT gmap-gmap.o -MD -MP -MF .deps/gmap-gmap.Tpo -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gmap.c: In function ‘apply_stage3’: gmap.c:3244:70: warning: passing argument 11 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types] 3244 | matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); | ^~~~~~~~ | | | Diagpool_T {aka struct Diagpool_T *} gmap.c:2672:82: note: expected ‘Cellpool_T’ {aka ‘struct Cellpool_T *’} but argument is of type ‘Diagpool_T’ {aka ‘struct Diagpool_T *’} 2672 | Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool, | ~~~~~~~~~~~^~~~~~~~ gmap.c:3244:79: warning: passing argument 12 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types] 3244 | matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); | ^~~~~~~~ | | | Cellpool_T {aka struct Cellpool_T *} gmap.c:2673:38: note: expected ‘Diagpool_T’ {aka ‘struct Diagpool_T *’} but argument is of type ‘Cellpool_T’ {aka ‘struct Cellpool_T *’} 2673 | Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) { | ~~~~~~~~~~~^~~~~~~~ mv -f .deps/gmap-gmap.Tpo .deps/gmap-gmap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm libtool: link: gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -O3 -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-genome_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-chrsubset.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-except.o -MD -MP -MF .deps/gmapl-except.Tpo -c -o gmapl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmapl-except.Tpo .deps/gmapl-except.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-assert.o -MD -MP -MF .deps/gmapl-assert.Tpo -c -o gmapl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmapl-assert.Tpo .deps/gmapl-assert.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-mem.o -MD -MP -MF .deps/gmapl-mem.Tpo -c -o gmapl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmapl-mem.Tpo .deps/gmapl-mem.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intlist.o -MD -MP -MF .deps/gmapl-intlist.Tpo -c -o gmapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmapl-intlist.Tpo .deps/gmapl-intlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-list.o -MD -MP -MF .deps/gmapl-list.Tpo -c -o gmapl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmapl-list.Tpo .deps/gmapl-list.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-littleendian.o -MD -MP -MF .deps/gmapl-littleendian.Tpo -c -o gmapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gmapl-littleendian.Tpo .deps/gmapl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bigendian.o -MD -MP -MF .deps/gmapl-bigendian.Tpo -c -o gmapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gmapl-bigendian.Tpo .deps/gmapl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-univinterval.o -MD -MP -MF .deps/gmapl-univinterval.Tpo -c -o gmapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/gmapl-univinterval.Tpo .deps/gmapl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-interval.o -MD -MP -MF .deps/gmapl-interval.Tpo -c -o gmapl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmapl-interval.Tpo .deps/gmapl-interval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uintlist.o -MD -MP -MF .deps/gmapl-uintlist.Tpo -c -o gmapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmapl-uintlist.Tpo .deps/gmapl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stopwatch.o -MD -MP -MF .deps/gmapl-stopwatch.Tpo -c -o gmapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmapl-stopwatch.Tpo .deps/gmapl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-access.o -MD -MP -MF .deps/gmapl-access.Tpo -c -o gmapl-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/gmapl-access.Tpo .deps/gmapl-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read-univ.o -MD -MP -MF .deps/gmapl-iit-read-univ.Tpo -c -o gmapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/gmapl-iit-read-univ.Tpo .deps/gmapl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-iit-read.o -MD -MP -MF .deps/gmapl-iit-read.Tpo -c -o gmapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gmapl-iit-read.Tpo .deps/gmapl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-md5.o -MD -MP -MF .deps/gmapl-md5.Tpo -c -o gmapl-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/gmapl-md5.Tpo .deps/gmapl-md5.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bzip2.o -MD -MP -MF .deps/gmapl-bzip2.Tpo -c -o gmapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmapl-bzip2.Tpo .deps/gmapl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-sequence.o -MD -MP -MF .deps/gmapl-sequence.Tpo -c -o gmapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmapl-sequence.Tpo .deps/gmapl-sequence.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-reader.o -MD -MP -MF .deps/gmapl-reader.Tpo -c -o gmapl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gmapl-reader.Tpo .deps/gmapl-reader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genomicpos.o -MD -MP -MF .deps/gmapl-genomicpos.Tpo -c -o gmapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmapl-genomicpos.Tpo .deps/gmapl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress.o -MD -MP -MF .deps/gmapl-compress.Tpo -c -o gmapl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmapl-compress.Tpo .deps/gmapl-compress.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-compress-write.o -MD -MP -MF .deps/gmapl-compress-write.Tpo -c -o gmapl-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c mv -f .deps/gmapl-compress-write.Tpo .deps/gmapl-compress-write.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gbuffer.o -MD -MP -MF .deps/gmapl-gbuffer.Tpo -c -o gmapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gmapl-gbuffer.Tpo .deps/gmapl-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome.o -MD -MP -MF .deps/gmapl-genome.Tpo -c -o gmapl-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/gmapl-genome.Tpo .deps/gmapl-genome.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_hr.o -MD -MP -MF .deps/gmapl-genome_hr.Tpo -c -o gmapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmapl-genome_hr.Tpo .deps/gmapl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome_sites.o -MD -MP -MF .deps/gmapl-genome_sites.Tpo -c -o gmapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gmapl-genome_sites.Tpo .deps/gmapl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-genome-write.o -MD -MP -MF .deps/gmapl-genome-write.Tpo -c -o gmapl-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c mv -f .deps/gmapl-genome-write.Tpo .deps/gmapl-genome-write.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-bitpack64-read.o -MD -MP -MF .deps/gmapl-bitpack64-read.Tpo -c -o gmapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmapl-bitpack64-read.Tpo .deps/gmapl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb.o -MD -MP -MF .deps/gmapl-indexdb.Tpo -c -o gmapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/gmapl-indexdb.Tpo .deps/gmapl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-indexdb_hr.o -MD -MP -MF .deps/gmapl-indexdb_hr.Tpo -c -o gmapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/gmapl-indexdb_hr.Tpo .deps/gmapl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligo.o -MD -MP -MF .deps/gmapl-oligo.Tpo -c -o gmapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gmapl-oligo.Tpo .deps/gmapl-oligo.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-block.o -MD -MP -MF .deps/gmapl-block.Tpo -c -o gmapl-block.o `test -f 'block.c' || echo './'`block.c mv -f .deps/gmapl-block.Tpo .deps/gmapl-block.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrom.o -MD -MP -MF .deps/gmapl-chrom.Tpo -c -o gmapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gmapl-chrom.Tpo .deps/gmapl-chrom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-segmentpos.o -MD -MP -MF .deps/gmapl-segmentpos.Tpo -c -o gmapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gmapl-segmentpos.Tpo .deps/gmapl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrnum.o -MD -MP -MF .deps/gmapl-chrnum.Tpo -c -o gmapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gmapl-chrnum.Tpo .deps/gmapl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chrsubset.o -MD -MP -MF .deps/gmapl-chrsubset.Tpo -c -o gmapl-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/gmapl-chrsubset.Tpo .deps/gmapl-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-uinttable.o -MD -MP -MF .deps/gmapl-uinttable.Tpo -c -o gmapl-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c mv -f .deps/gmapl-uinttable.Tpo .deps/gmapl-uinttable.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gregion.o -MD -MP -MF .deps/gmapl-gregion.Tpo -c -o gmapl-gregion.o `test -f 'gregion.c' || echo './'`gregion.c mv -f .deps/gmapl-gregion.Tpo .deps/gmapl-gregion.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-match.o -MD -MP -MF .deps/gmapl-match.Tpo -c -o gmapl-match.o `test -f 'match.c' || echo './'`match.c mv -f .deps/gmapl-match.Tpo .deps/gmapl-match.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-matchpool.o -MD -MP -MF .deps/gmapl-matchpool.Tpo -c -o gmapl-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c mv -f .deps/gmapl-matchpool.Tpo .deps/gmapl-matchpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagnostic.o -MD -MP -MF .deps/gmapl-diagnostic.Tpo -c -o gmapl-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c mv -f .deps/gmapl-diagnostic.Tpo .deps/gmapl-diagnostic.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage1.o -MD -MP -MF .deps/gmapl-stage1.Tpo -c -o gmapl-stage1.o `test -f 'stage1.c' || echo './'`stage1.c mv -f .deps/gmapl-stage1.Tpo .deps/gmapl-stage1.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diag.o -MD -MP -MF .deps/gmapl-diag.Tpo -c -o gmapl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gmapl-diag.Tpo .deps/gmapl-diag.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-diagpool.o -MD -MP -MF .deps/gmapl-diagpool.Tpo -c -o gmapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gmapl-diagpool.Tpo .deps/gmapl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cmet.o -MD -MP -MF .deps/gmapl-cmet.Tpo -c -o gmapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gmapl-cmet.Tpo .deps/gmapl-cmet.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-atoi.o -MD -MP -MF .deps/gmapl-atoi.Tpo -c -o gmapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gmapl-atoi.Tpo .deps/gmapl-atoi.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-orderstat.o -MD -MP -MF .deps/gmapl-orderstat.Tpo -c -o gmapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gmapl-orderstat.Tpo .deps/gmapl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-oligoindex_hr.o -MD -MP -MF .deps/gmapl-oligoindex_hr.Tpo -c -o gmapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gmapl-oligoindex_hr.Tpo .deps/gmapl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-intron.o -MD -MP -MF .deps/gmapl-intron.Tpo -c -o gmapl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gmapl-intron.Tpo .deps/gmapl-intron.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent.o -MD -MP -MF .deps/gmapl-maxent.Tpo -c -o gmapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gmapl-maxent.Tpo .deps/gmapl-maxent.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-maxent_hr.o -MD -MP -MF .deps/gmapl-maxent_hr.Tpo -c -o gmapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gmapl-maxent_hr.Tpo .deps/gmapl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pair.o -MD -MP -MF .deps/gmapl-pair.Tpo -c -o gmapl-pair.o `test -f 'pair.c' || echo './'`pair.c mv -f .deps/gmapl-pair.Tpo .deps/gmapl-pair.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pairpool.o -MD -MP -MF .deps/gmapl-pairpool.Tpo -c -o gmapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gmapl-pairpool.Tpo .deps/gmapl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-cellpool.o -MD -MP -MF .deps/gmapl-cellpool.Tpo -c -o gmapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gmapl-cellpool.Tpo .deps/gmapl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage2.o -MD -MP -MF .deps/gmapl-stage2.Tpo -c -o gmapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gmapl-stage2.Tpo .deps/gmapl-stage2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-doublelist.o -MD -MP -MF .deps/gmapl-doublelist.Tpo -c -o gmapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gmapl-doublelist.Tpo .deps/gmapl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-smooth.o -MD -MP -MF .deps/gmapl-smooth.Tpo -c -o gmapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gmapl-smooth.Tpo .deps/gmapl-smooth.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicestringpool.o -MD -MP -MF .deps/gmapl-splicestringpool.Tpo -c -o gmapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gmapl-splicestringpool.Tpo .deps/gmapl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie_build.o -MD -MP -MF .deps/gmapl-splicetrie_build.Tpo -c -o gmapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gmapl-splicetrie_build.Tpo .deps/gmapl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-splicetrie.o -MD -MP -MF .deps/gmapl-splicetrie.Tpo -c -o gmapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gmapl-splicetrie.Tpo .deps/gmapl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-boyer-moore.o -MD -MP -MF .deps/gmapl-boyer-moore.Tpo -c -o gmapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gmapl-boyer-moore.Tpo .deps/gmapl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-dynprog.o -MD -MP -MF .deps/gmapl-dynprog.Tpo -c -o gmapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gmapl-dynprog.Tpo .deps/gmapl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-translation.o -MD -MP -MF .deps/gmapl-translation.Tpo -c -o gmapl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gmapl-translation.Tpo .deps/gmapl-translation.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-pbinom.o -MD -MP -MF .deps/gmapl-pbinom.Tpo -c -o gmapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gmapl-pbinom.Tpo .deps/gmapl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-changepoint.o -MD -MP -MF .deps/gmapl-changepoint.Tpo -c -o gmapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gmapl-changepoint.Tpo .deps/gmapl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-stage3.o -MD -MP -MF .deps/gmapl-stage3.Tpo -c -o gmapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gmapl-stage3.Tpo .deps/gmapl-stage3.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-request.o -MD -MP -MF .deps/gmapl-request.Tpo -c -o gmapl-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gmapl-request.Tpo .deps/gmapl-request.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-result.o -MD -MP -MF .deps/gmapl-result.Tpo -c -o gmapl-result.o `test -f 'result.c' || echo './'`result.c mv -f .deps/gmapl-result.Tpo .deps/gmapl-result.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-inbuffer.o -MD -MP -MF .deps/gmapl-inbuffer.Tpo -c -o gmapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gmapl-inbuffer.Tpo .deps/gmapl-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-samheader.o -MD -MP -MF .deps/gmapl-samheader.Tpo -c -o gmapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gmapl-samheader.Tpo .deps/gmapl-samheader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-outbuffer.o -MD -MP -MF .deps/gmapl-outbuffer.Tpo -c -o gmapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gmapl-outbuffer.Tpo .deps/gmapl-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-chimera.o -MD -MP -MF .deps/gmapl-chimera.Tpo -c -o gmapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gmapl-chimera.Tpo .deps/gmapl-chimera.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-datadir.o -MD -MP -MF .deps/gmapl-datadir.Tpo -c -o gmapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gmapl-datadir.Tpo .deps/gmapl-datadir.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt.o -MD -MP -MF .deps/gmapl-getopt.Tpo -c -o gmapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gmapl-getopt.Tpo .deps/gmapl-getopt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-getopt1.o -MD -MP -MF .deps/gmapl-getopt1.Tpo -c -o gmapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gmapl-getopt1.Tpo .deps/gmapl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -MT gmapl-gmap.o -MD -MP -MF .deps/gmapl-gmap.Tpo -c -o gmapl-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gmap.c: In function ‘apply_stage3’: gmap.c:3244:70: warning: passing argument 11 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types] 3244 | matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); | ^~~~~~~~ | | | Diagpool_T {aka struct Diagpool_T *} gmap.c:2672:82: note: expected ‘Cellpool_T’ {aka ‘struct Cellpool_T *’} but argument is of type ‘Diagpool_T’ {aka ‘struct Diagpool_T *’} 2672 | Matchpool_T matchpool, Pairpool_T pairpool, Cellpool_T cellpool, | ~~~~~~~~~~~^~~~~~~~ gmap.c:3244:79: warning: passing argument 12 of ‘check_middle_piece_local’ from incompatible pointer type [-Wincompatible-pointer-types] 3244 | matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR); | ^~~~~~~~ | | | Cellpool_T {aka struct Cellpool_T *} gmap.c:2673:38: note: expected ‘Diagpool_T’ {aka ‘struct Diagpool_T *’} but argument is of type ‘Cellpool_T’ {aka ‘struct Cellpool_T *’} 2673 | Diagpool_T diagpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) { | ~~~~~~~~~~~^~~~~~~~ mv -f .deps/gmapl-gmap.Tpo .deps/gmapl-gmap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm libtool: link: gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DLARGE_GENOMES=1 -O3 -o gmapl gmapl-except.o gmapl-assert.o gmapl-mem.o gmapl-intlist.o gmapl-list.o gmapl-littleendian.o gmapl-bigendian.o gmapl-univinterval.o gmapl-interval.o gmapl-uintlist.o gmapl-stopwatch.o gmapl-access.o gmapl-iit-read-univ.o gmapl-iit-read.o gmapl-md5.o gmapl-bzip2.o gmapl-sequence.o gmapl-reader.o gmapl-genomicpos.o gmapl-compress.o gmapl-compress-write.o gmapl-gbuffer.o gmapl-genome.o gmapl-genome_hr.o gmapl-genome_sites.o gmapl-genome-write.o gmapl-bitpack64-read.o gmapl-indexdb.o gmapl-indexdb_hr.o gmapl-oligo.o gmapl-block.o gmapl-chrom.o gmapl-segmentpos.o gmapl-chrnum.o gmapl-chrsubset.o gmapl-uinttable.o gmapl-gregion.o gmapl-match.o gmapl-matchpool.o gmapl-diagnostic.o gmapl-stage1.o gmapl-diag.o gmapl-diagpool.o gmapl-cmet.o gmapl-atoi.o gmapl-orderstat.o gmapl-oligoindex_hr.o gmapl-intron.o gmapl-maxent.o gmapl-maxent_hr.o gmapl-pair.o gmapl-pairpool.o gmapl-cellpool.o gmapl-stage2.o gmapl-doublelist.o gmapl-smooth.o gmapl-splicestringpool.o gmapl-splicetrie_build.o gmapl-splicetrie.o gmapl-boyer-moore.o gmapl-dynprog.o gmapl-translation.o gmapl-pbinom.o gmapl-changepoint.o gmapl-stage3.o gmapl-request.o gmapl-result.o gmapl-inbuffer.o gmapl-samheader.o gmapl-outbuffer.o gmapl-chimera.o gmapl-datadir.o gmapl-getopt.o gmapl-getopt1.o gmapl-gmap.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-except.o -MD -MP -MF .deps/get_genome-except.Tpo -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/get_genome-except.Tpo .deps/get_genome-except.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-assert.o -MD -MP -MF .deps/get_genome-assert.Tpo -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/get_genome-assert.Tpo .deps/get_genome-assert.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-mem.o -MD -MP -MF .deps/get_genome-mem.Tpo -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/get_genome-mem.Tpo .deps/get_genome-mem.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-intlist.o -MD -MP -MF .deps/get_genome-intlist.Tpo -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/get_genome-intlist.Tpo .deps/get_genome-intlist.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-list.o -MD -MP -MF .deps/get_genome-list.Tpo -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/get_genome-list.Tpo .deps/get_genome-list.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-littleendian.o -MD -MP -MF .deps/get_genome-littleendian.Tpo -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/get_genome-littleendian.Tpo .deps/get_genome-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bigendian.o -MD -MP -MF .deps/get_genome-bigendian.Tpo -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/get_genome-bigendian.Tpo .deps/get_genome-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-univinterval.o -MD -MP -MF .deps/get_genome-univinterval.Tpo -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/get_genome-univinterval.Tpo .deps/get_genome-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-interval.o -MD -MP -MF .deps/get_genome-interval.Tpo -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/get_genome-interval.Tpo .deps/get_genome-interval.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-uintlist.o -MD -MP -MF .deps/get_genome-uintlist.Tpo -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/get_genome-uintlist.Tpo .deps/get_genome-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-stopwatch.o -MD -MP -MF .deps/get_genome-stopwatch.Tpo -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/get_genome-stopwatch.Tpo .deps/get_genome-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-access.o -MD -MP -MF .deps/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/get_genome-access.Tpo .deps/get_genome-access.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read-univ.o -MD -MP -MF .deps/get_genome-iit-read-univ.Tpo -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/get_genome-iit-read-univ.Tpo .deps/get_genome-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-iit-read.o -MD -MP -MF .deps/get_genome-iit-read.Tpo -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/get_genome-iit-read.Tpo .deps/get_genome-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-md5.o -MD -MP -MF .deps/get_genome-md5.Tpo -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/get_genome-md5.Tpo .deps/get_genome-md5.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-bzip2.o -MD -MP -MF .deps/get_genome-bzip2.Tpo -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/get_genome-bzip2.Tpo .deps/get_genome-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-sequence.o -MD -MP -MF .deps/get_genome-sequence.Tpo -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/get_genome-sequence.Tpo .deps/get_genome-sequence.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genome.o -MD -MP -MF .deps/get_genome-genome.Tpo -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/get_genome-genome.Tpo .deps/get_genome-genome.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-genomicpos.o -MD -MP -MF .deps/get_genome-genomicpos.Tpo -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/get_genome-genomicpos.Tpo .deps/get_genome-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrom.o -MD -MP -MF .deps/get_genome-chrom.Tpo -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/get_genome-chrom.Tpo .deps/get_genome-chrom.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrnum.o -MD -MP -MF .deps/get_genome-chrnum.Tpo -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/get_genome-chrnum.Tpo .deps/get_genome-chrnum.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-chrsubset.o -MD -MP -MF .deps/get_genome-chrsubset.Tpo -c -o get_genome-chrsubset.o `test -f 'chrsubset.c' || echo './'`chrsubset.c mv -f .deps/get_genome-chrsubset.Tpo .deps/get_genome-chrsubset.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-datadir.o -MD -MP -MF .deps/get_genome-datadir.Tpo -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/get_genome-datadir.Tpo .deps/get_genome-datadir.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-parserange.o -MD -MP -MF .deps/get_genome-parserange.Tpo -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c mv -f .deps/get_genome-parserange.Tpo .deps/get_genome-parserange.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt.o -MD -MP -MF .deps/get_genome-getopt.Tpo -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/get_genome-getopt.Tpo .deps/get_genome-getopt.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-getopt1.o -MD -MP -MF .deps/get_genome-getopt1.Tpo -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/get_genome-getopt1.Tpo .deps/get_genome-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT get_genome-get-genome.o -MD -MP -MF .deps/get_genome-get-genome.Tpo -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c mv -f .deps/get_genome-get-genome.Tpo .deps/get_genome-get-genome.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm libtool: link: gcc -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-access.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-chrsubset.o get_genome-datadir.o get_genome-parserange.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-except.o -MD -MP -MF .deps/gmapindex-except.Tpo -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gmapindex-except.Tpo .deps/gmapindex-except.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-assert.o -MD -MP -MF .deps/gmapindex-assert.Tpo -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gmapindex-assert.Tpo .deps/gmapindex-assert.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-mem.o -MD -MP -MF .deps/gmapindex-mem.Tpo -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gmapindex-mem.Tpo .deps/gmapindex-mem.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-intlist.o -MD -MP -MF .deps/gmapindex-intlist.Tpo -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gmapindex-intlist.Tpo .deps/gmapindex-intlist.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-list.o -MD -MP -MF .deps/gmapindex-list.Tpo -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gmapindex-list.Tpo .deps/gmapindex-list.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-littleendian.o -MD -MP -MF .deps/gmapindex-littleendian.Tpo -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gmapindex-littleendian.Tpo .deps/gmapindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-bigendian.o -MD -MP -MF .deps/gmapindex-bigendian.Tpo -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gmapindex-bigendian.Tpo .deps/gmapindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-univinterval.o -MD -MP -MF .deps/gmapindex-univinterval.Tpo -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/gmapindex-univinterval.Tpo .deps/gmapindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-interval.o -MD -MP -MF .deps/gmapindex-interval.Tpo -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gmapindex-interval.Tpo .deps/gmapindex-interval.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-uintlist.o -MD -MP -MF .deps/gmapindex-uintlist.Tpo -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gmapindex-uintlist.Tpo .deps/gmapindex-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-stopwatch.o -MD -MP -MF .deps/gmapindex-stopwatch.Tpo -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gmapindex-stopwatch.Tpo .deps/gmapindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-access.o -MD -MP -MF .deps/gmapindex-access.Tpo -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/gmapindex-access.Tpo .deps/gmapindex-access.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-iit-read-univ.o -MD -MP -MF .deps/gmapindex-iit-read-univ.Tpo -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/gmapindex-iit-read-univ.Tpo .deps/gmapindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-iit-write-univ.o -MD -MP -MF .deps/gmapindex-iit-write-univ.Tpo -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c mv -f .deps/gmapindex-iit-write-univ.Tpo .deps/gmapindex-iit-write-univ.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-iit-read.o -MD -MP -MF .deps/gmapindex-iit-read.Tpo -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gmapindex-iit-read.Tpo .deps/gmapindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-md5.o -MD -MP -MF .deps/gmapindex-md5.Tpo -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/gmapindex-md5.Tpo .deps/gmapindex-md5.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-bzip2.o -MD -MP -MF .deps/gmapindex-bzip2.Tpo -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gmapindex-bzip2.Tpo .deps/gmapindex-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-sequence.o -MD -MP -MF .deps/gmapindex-sequence.Tpo -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gmapindex-sequence.Tpo .deps/gmapindex-sequence.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-genome.o -MD -MP -MF .deps/gmapindex-genome.Tpo -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/gmapindex-genome.Tpo .deps/gmapindex-genome.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-genomicpos.o -MD -MP -MF .deps/gmapindex-genomicpos.Tpo -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gmapindex-genomicpos.Tpo .deps/gmapindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-compress-write.o -MD -MP -MF .deps/gmapindex-compress-write.Tpo -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c mv -f .deps/gmapindex-compress-write.Tpo .deps/gmapindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-genome-write.o -MD -MP -MF .deps/gmapindex-genome-write.Tpo -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c mv -f .deps/gmapindex-genome-write.Tpo .deps/gmapindex-genome-write.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-compress.o -MD -MP -MF .deps/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gmapindex-compress.Tpo .deps/gmapindex-compress.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-genome_hr.o -MD -MP -MF .deps/gmapindex-genome_hr.Tpo -c -o gmapindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gmapindex-genome_hr.Tpo .deps/gmapindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-read.o -MD -MP -MF .deps/gmapindex-bitpack64-read.Tpo -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gmapindex-bitpack64-read.Tpo .deps/gmapindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-bitpack64-write.o -MD -MP -MF .deps/gmapindex-bitpack64-write.Tpo -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c: In function ‘Bitpack64_write_vert’: bitpack64-write.c:4146:38: warning: passing argument 2 of ‘reorder_values_vertically’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4146 | reorder_values_vertically(vertical,horizontal); | ^~~~~~~~~~ bitpack64-write.c:4091:70: note: expected ‘Positionsptr_T *’ {aka ‘unsigned int *’} but argument is of type ‘const UINT4 *’ {aka ‘const unsigned int *’} 4091 | reorder_values_vertically (Positionsptr_T *vertical, Positionsptr_T *horizontal) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~ mv -f .deps/gmapindex-bitpack64-write.Tpo .deps/gmapindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-indexdb.o -MD -MP -MF .deps/gmapindex-indexdb.Tpo -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/gmapindex-indexdb.Tpo .deps/gmapindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-indexdb-write.o -MD -MP -MF .deps/gmapindex-indexdb-write.Tpo -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c mv -f .deps/gmapindex-indexdb-write.Tpo .deps/gmapindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-table.o -MD -MP -MF .deps/gmapindex-table.Tpo -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c table.c: In function ‘Table_gc’: table.c:283:18: warning: passing argument 1 of ‘keyfree’ from incompatible pointer type [-Wincompatible-pointer-types] 283 | (*keyfree)(&p->key); | ^~~~~~~ | | | const void ** table.c:283:18: note: expected ‘void **’ but argument is of type ‘const void **’ mv -f .deps/gmapindex-table.Tpo .deps/gmapindex-table.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-tableuint.o -MD -MP -MF .deps/gmapindex-tableuint.Tpo -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c mv -f .deps/gmapindex-tableuint.Tpo .deps/gmapindex-tableuint.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-tableuint8.o -MD -MP -MF .deps/gmapindex-tableuint8.Tpo -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c mv -f .deps/gmapindex-tableuint8.Tpo .deps/gmapindex-tableuint8.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-chrom.o -MD -MP -MF .deps/gmapindex-chrom.Tpo -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gmapindex-chrom.Tpo .deps/gmapindex-chrom.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-segmentpos.o -MD -MP -MF .deps/gmapindex-segmentpos.Tpo -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gmapindex-segmentpos.Tpo .deps/gmapindex-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-saca-k.o -MD -MP -MF .deps/gmapindex-saca-k.Tpo -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo './'`saca-k.c mv -f .deps/gmapindex-saca-k.Tpo .deps/gmapindex-saca-k.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-sarray-write.o -MD -MP -MF .deps/gmapindex-sarray-write.Tpo -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo './'`sarray-write.c mv -f .deps/gmapindex-sarray-write.Tpo .deps/gmapindex-sarray-write.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT gmapindex-gmapindex.o -MD -MP -MF .deps/gmapindex-gmapindex.Tpo -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c mv -f .deps/gmapindex-gmapindex.Tpo .deps/gmapindex-gmapindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DUTILITYP=1 -O3 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o -lz -lbz2 -lm libtool: link: gcc -DUTILITYP=1 -O3 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-access.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-genome_hr.o gmapindex-bitpack64-read.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-saca-k.o gmapindex-sarray-write.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-except.o -MD -MP -MF .deps/iit_store-except.Tpo -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_store-except.Tpo .deps/iit_store-except.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-assert.o -MD -MP -MF .deps/iit_store-assert.Tpo -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_store-assert.Tpo .deps/iit_store-assert.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-mem.o -MD -MP -MF .deps/iit_store-mem.Tpo -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_store-mem.Tpo .deps/iit_store-mem.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-intlist.o -MD -MP -MF .deps/iit_store-intlist.Tpo -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_store-intlist.Tpo .deps/iit_store-intlist.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-list.o -MD -MP -MF .deps/iit_store-list.Tpo -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_store-list.Tpo .deps/iit_store-list.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-littleendian.o -MD -MP -MF .deps/iit_store-littleendian.Tpo -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/iit_store-littleendian.Tpo .deps/iit_store-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-bigendian.o -MD -MP -MF .deps/iit_store-bigendian.Tpo -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/iit_store-bigendian.Tpo .deps/iit_store-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-univinterval.o -MD -MP -MF .deps/iit_store-univinterval.Tpo -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/iit_store-univinterval.Tpo .deps/iit_store-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-interval.o -MD -MP -MF .deps/iit_store-interval.Tpo -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_store-interval.Tpo .deps/iit_store-interval.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-uintlist.o -MD -MP -MF .deps/iit_store-uintlist.Tpo -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_store-uintlist.Tpo .deps/iit_store-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-stopwatch.o -MD -MP -MF .deps/iit_store-stopwatch.Tpo -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_store-stopwatch.Tpo .deps/iit_store-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-access.o -MD -MP -MF .deps/iit_store-access.Tpo -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/iit_store-access.Tpo .deps/iit_store-access.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-iit-write-univ.o -MD -MP -MF .deps/iit_store-iit-write-univ.Tpo -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c mv -f .deps/iit_store-iit-write-univ.Tpo .deps/iit_store-iit-write-univ.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-iit-write.o -MD -MP -MF .deps/iit_store-iit-write.Tpo -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c mv -f .deps/iit_store-iit-write.Tpo .deps/iit_store-iit-write.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-tableint.o -MD -MP -MF .deps/iit_store-tableint.Tpo -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c mv -f .deps/iit_store-tableint.Tpo .deps/iit_store-tableint.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-table.o -MD -MP -MF .deps/iit_store-table.Tpo -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c table.c: In function ‘Table_gc’: table.c:283:18: warning: passing argument 1 of ‘keyfree’ from incompatible pointer type [-Wincompatible-pointer-types] 283 | (*keyfree)(&p->key); | ^~~~~~~ | | | const void ** table.c:283:18: note: expected ‘void **’ but argument is of type ‘const void **’ mv -f .deps/iit_store-table.Tpo .deps/iit_store-table.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-chrom.o -MD -MP -MF .deps/iit_store-chrom.Tpo -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/iit_store-chrom.Tpo .deps/iit_store-chrom.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-getopt.o -MD -MP -MF .deps/iit_store-getopt.Tpo -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/iit_store-getopt.Tpo .deps/iit_store-getopt.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-getopt1.o -MD -MP -MF .deps/iit_store-getopt1.Tpo -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/iit_store-getopt1.Tpo .deps/iit_store-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_store-iit_store.o -MD -MP -MF .deps/iit_store-iit_store.Tpo -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c mv -f .deps/iit_store-iit_store.Tpo .deps/iit_store-iit_store.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DUTILITYP=1 -O3 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm libtool: link: gcc -DUTILITYP=1 -O3 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-access.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lm gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-except.o -MD -MP -MF .deps/iit_get-except.Tpo -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_get-except.Tpo .deps/iit_get-except.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-assert.o -MD -MP -MF .deps/iit_get-assert.Tpo -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_get-assert.Tpo .deps/iit_get-assert.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-mem.o -MD -MP -MF .deps/iit_get-mem.Tpo -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_get-mem.Tpo .deps/iit_get-mem.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-intlist.o -MD -MP -MF .deps/iit_get-intlist.Tpo -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_get-intlist.Tpo .deps/iit_get-intlist.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-list.o -MD -MP -MF .deps/iit_get-list.Tpo -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_get-list.Tpo .deps/iit_get-list.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-littleendian.o -MD -MP -MF .deps/iit_get-littleendian.Tpo -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/iit_get-littleendian.Tpo .deps/iit_get-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-bigendian.o -MD -MP -MF .deps/iit_get-bigendian.Tpo -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/iit_get-bigendian.Tpo .deps/iit_get-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-univinterval.o -MD -MP -MF .deps/iit_get-univinterval.Tpo -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/iit_get-univinterval.Tpo .deps/iit_get-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-interval.o -MD -MP -MF .deps/iit_get-interval.Tpo -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_get-interval.Tpo .deps/iit_get-interval.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-uintlist.o -MD -MP -MF .deps/iit_get-uintlist.Tpo -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_get-uintlist.Tpo .deps/iit_get-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-stopwatch.o -MD -MP -MF .deps/iit_get-stopwatch.Tpo -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_get-stopwatch.Tpo .deps/iit_get-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-access.o -MD -MP -MF .deps/iit_get-access.Tpo -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/iit_get-access.Tpo .deps/iit_get-access.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-iit-read-univ.o -MD -MP -MF .deps/iit_get-iit-read-univ.Tpo -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/iit_get-iit-read-univ.Tpo .deps/iit_get-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-iit-read.o -MD -MP -MF .deps/iit_get-iit-read.Tpo -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/iit_get-iit-read.Tpo .deps/iit_get-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-parserange.o -MD -MP -MF .deps/iit_get-parserange.Tpo -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c mv -f .deps/iit_get-parserange.Tpo .deps/iit_get-parserange.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-getopt.o -MD -MP -MF .deps/iit_get-getopt.Tpo -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/iit_get-getopt.Tpo .deps/iit_get-getopt.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-getopt1.o -MD -MP -MF .deps/iit_get-getopt1.Tpo -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/iit_get-getopt1.Tpo .deps/iit_get-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_get-iit_get.o -MD -MP -MF .deps/iit_get-iit_get.Tpo -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c mv -f .deps/iit_get-iit_get.Tpo .deps/iit_get-iit_get.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DUTILITYP=1 -O3 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm libtool: link: gcc -DUTILITYP=1 -O3 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-access.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lm gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-except.o -MD -MP -MF .deps/iit_dump-except.Tpo -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/iit_dump-except.Tpo .deps/iit_dump-except.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-assert.o -MD -MP -MF .deps/iit_dump-assert.Tpo -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/iit_dump-assert.Tpo .deps/iit_dump-assert.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-mem.o -MD -MP -MF .deps/iit_dump-mem.Tpo -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/iit_dump-mem.Tpo .deps/iit_dump-mem.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-littleendian.o -MD -MP -MF .deps/iit_dump-littleendian.Tpo -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/iit_dump-littleendian.Tpo .deps/iit_dump-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-bigendian.o -MD -MP -MF .deps/iit_dump-bigendian.Tpo -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/iit_dump-bigendian.Tpo .deps/iit_dump-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-intlist.o -MD -MP -MF .deps/iit_dump-intlist.Tpo -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/iit_dump-intlist.Tpo .deps/iit_dump-intlist.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-list.o -MD -MP -MF .deps/iit_dump-list.Tpo -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/iit_dump-list.Tpo .deps/iit_dump-list.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-univinterval.o -MD -MP -MF .deps/iit_dump-univinterval.Tpo -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/iit_dump-univinterval.Tpo .deps/iit_dump-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-interval.o -MD -MP -MF .deps/iit_dump-interval.Tpo -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/iit_dump-interval.Tpo .deps/iit_dump-interval.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-uintlist.o -MD -MP -MF .deps/iit_dump-uintlist.Tpo -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/iit_dump-uintlist.Tpo .deps/iit_dump-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-stopwatch.o -MD -MP -MF .deps/iit_dump-stopwatch.Tpo -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/iit_dump-stopwatch.Tpo .deps/iit_dump-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-access.o -MD -MP -MF .deps/iit_dump-access.Tpo -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/iit_dump-access.Tpo .deps/iit_dump-access.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-iit-read-univ.o -MD -MP -MF .deps/iit_dump-iit-read-univ.Tpo -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/iit_dump-iit-read-univ.Tpo .deps/iit_dump-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-iit-read.o -MD -MP -MF .deps/iit_dump-iit-read.Tpo -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/iit_dump-iit-read.Tpo .deps/iit_dump-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-getopt.o -MD -MP -MF .deps/iit_dump-getopt.Tpo -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/iit_dump-getopt.Tpo .deps/iit_dump-getopt.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-getopt1.o -MD -MP -MF .deps/iit_dump-getopt1.Tpo -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/iit_dump-getopt1.Tpo .deps/iit_dump-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DUTILITYP=1 -O3 -MT iit_dump-iit_dump.o -MD -MP -MF .deps/iit_dump-iit_dump.Tpo -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c mv -f .deps/iit_dump-iit_dump.Tpo .deps/iit_dump-iit_dump.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DUTILITYP=1 -O3 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm libtool: link: gcc -DUTILITYP=1 -O3 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-access.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-except.o -MD -MP -MF .deps/gsnap-except.Tpo -c -o gsnap-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gsnap-except.Tpo .deps/gsnap-except.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-assert.o -MD -MP -MF .deps/gsnap-assert.Tpo -c -o gsnap-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gsnap-assert.Tpo .deps/gsnap-assert.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mem.o -MD -MP -MF .deps/gsnap-mem.Tpo -c -o gsnap-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gsnap-mem.Tpo .deps/gsnap-mem.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intlist.o -MD -MP -MF .deps/gsnap-intlist.Tpo -c -o gsnap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gsnap-intlist.Tpo .deps/gsnap-intlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-list.o -MD -MP -MF .deps/gsnap-list.Tpo -c -o gsnap-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gsnap-list.Tpo .deps/gsnap-list.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-littleendian.o -MD -MP -MF .deps/gsnap-littleendian.Tpo -c -o gsnap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gsnap-littleendian.Tpo .deps/gsnap-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bigendian.o -MD -MP -MF .deps/gsnap-bigendian.Tpo -c -o gsnap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gsnap-bigendian.Tpo .deps/gsnap-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-univinterval.o -MD -MP -MF .deps/gsnap-univinterval.Tpo -c -o gsnap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/gsnap-univinterval.Tpo .deps/gsnap-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-interval.o -MD -MP -MF .deps/gsnap-interval.Tpo -c -o gsnap-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gsnap-interval.Tpo .deps/gsnap-interval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-uintlist.o -MD -MP -MF .deps/gsnap-uintlist.Tpo -c -o gsnap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gsnap-uintlist.Tpo .deps/gsnap-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stopwatch.o -MD -MP -MF .deps/gsnap-stopwatch.Tpo -c -o gsnap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gsnap-stopwatch.Tpo .deps/gsnap-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-access.o -MD -MP -MF .deps/gsnap-access.Tpo -c -o gsnap-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/gsnap-access.Tpo .deps/gsnap-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read-univ.o -MD -MP -MF .deps/gsnap-iit-read-univ.Tpo -c -o gsnap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/gsnap-iit-read-univ.Tpo .deps/gsnap-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-iit-read.o -MD -MP -MF .deps/gsnap-iit-read.Tpo -c -o gsnap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gsnap-iit-read.Tpo .deps/gsnap-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-md5.o -MD -MP -MF .deps/gsnap-md5.Tpo -c -o gsnap-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/gsnap-md5.Tpo .deps/gsnap-md5.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bzip2.o -MD -MP -MF .deps/gsnap-bzip2.Tpo -c -o gsnap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gsnap-bzip2.Tpo .deps/gsnap-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sequence.o -MD -MP -MF .deps/gsnap-sequence.Tpo -c -o gsnap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gsnap-sequence.Tpo .deps/gsnap-sequence.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-reader.o -MD -MP -MF .deps/gsnap-reader.Tpo -c -o gsnap-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gsnap-reader.Tpo .deps/gsnap-reader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genomicpos.o -MD -MP -MF .deps/gsnap-genomicpos.Tpo -c -o gsnap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gsnap-genomicpos.Tpo .deps/gsnap-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-compress.o -MD -MP -MF .deps/gsnap-compress.Tpo -c -o gsnap-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gsnap-compress.Tpo .deps/gsnap-compress.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome.o -MD -MP -MF .deps/gsnap-genome.Tpo -c -o gsnap-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/gsnap-genome.Tpo .deps/gsnap-genome.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_hr.o -MD -MP -MF .deps/gsnap-genome_hr.Tpo -c -o gsnap-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gsnap-genome_hr.Tpo .deps/gsnap-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-genome_sites.o -MD -MP -MF .deps/gsnap-genome_sites.Tpo -c -o gsnap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gsnap-genome_sites.Tpo .deps/gsnap-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-read.o -MD -MP -MF .deps/gsnap-bitpack64-read.Tpo -c -o gsnap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gsnap-bitpack64-read.Tpo .deps/gsnap-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb.o -MD -MP -MF .deps/gsnap-indexdb.Tpo -c -o gsnap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/gsnap-indexdb.Tpo .deps/gsnap-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indexdb_hr.o -MD -MP -MF .deps/gsnap-indexdb_hr.Tpo -c -o gsnap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/gsnap-indexdb_hr.Tpo .deps/gsnap-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligo.o -MD -MP -MF .deps/gsnap-oligo.Tpo -c -o gsnap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gsnap-oligo.Tpo .deps/gsnap-oligo.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrom.o -MD -MP -MF .deps/gsnap-chrom.Tpo -c -o gsnap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gsnap-chrom.Tpo .deps/gsnap-chrom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-segmentpos.o -MD -MP -MF .deps/gsnap-segmentpos.Tpo -c -o gsnap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gsnap-segmentpos.Tpo .deps/gsnap-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chrnum.o -MD -MP -MF .deps/gsnap-chrnum.Tpo -c -o gsnap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gsnap-chrnum.Tpo .deps/gsnap-chrnum.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent_hr.o -MD -MP -MF .deps/gsnap-maxent_hr.Tpo -c -o gsnap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gsnap-maxent_hr.Tpo .deps/gsnap-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samprint.o -MD -MP -MF .deps/gsnap-samprint.Tpo -c -o gsnap-samprint.o `test -f 'samprint.c' || echo './'`samprint.c mv -f .deps/gsnap-samprint.Tpo .deps/gsnap-samprint.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-mapq.o -MD -MP -MF .deps/gsnap-mapq.Tpo -c -o gsnap-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/gsnap-mapq.Tpo .deps/gsnap-mapq.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-shortread.o -MD -MP -MF .deps/gsnap-shortread.Tpo -c -o gsnap-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/gsnap-shortread.Tpo .deps/gsnap-shortread.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-substring.o -MD -MP -MF .deps/gsnap-substring.Tpo -c -o gsnap-substring.o `test -f 'substring.c' || echo './'`substring.c mv -f .deps/gsnap-substring.Tpo .deps/gsnap-substring.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3hr.o -MD -MP -MF .deps/gsnap-stage3hr.Tpo -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/gsnap-stage3hr.Tpo .deps/gsnap-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-goby.o -MD -MP -MF .deps/gsnap-goby.Tpo -c -o gsnap-goby.o `test -f 'goby.c' || echo './'`goby.c mv -f .deps/gsnap-goby.Tpo .deps/gsnap-goby.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-spanningelt.o -MD -MP -MF .deps/gsnap-spanningelt.Tpo -c -o gsnap-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/gsnap-spanningelt.Tpo .deps/gsnap-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cmet.o -MD -MP -MF .deps/gsnap-cmet.Tpo -c -o gsnap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gsnap-cmet.Tpo .deps/gsnap-cmet.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-atoi.o -MD -MP -MF .deps/gsnap-atoi.Tpo -c -o gsnap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gsnap-atoi.Tpo .deps/gsnap-atoi.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-maxent.o -MD -MP -MF .deps/gsnap-maxent.Tpo -c -o gsnap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gsnap-maxent.Tpo .deps/gsnap-maxent.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pair.o -MD -MP -MF .deps/gsnap-pair.Tpo -c -o gsnap-pair.o `test -f 'pair.c' || echo './'`pair.c mv -f .deps/gsnap-pair.Tpo .deps/gsnap-pair.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pairpool.o -MD -MP -MF .deps/gsnap-pairpool.Tpo -c -o gsnap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gsnap-pairpool.Tpo .deps/gsnap-pairpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diag.o -MD -MP -MF .deps/gsnap-diag.Tpo -c -o gsnap-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gsnap-diag.Tpo .deps/gsnap-diag.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-diagpool.o -MD -MP -MF .deps/gsnap-diagpool.Tpo -c -o gsnap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gsnap-diagpool.Tpo .deps/gsnap-diagpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-orderstat.o -MD -MP -MF .deps/gsnap-orderstat.Tpo -c -o gsnap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gsnap-orderstat.Tpo .deps/gsnap-orderstat.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-oligoindex_hr.o -MD -MP -MF .deps/gsnap-oligoindex_hr.Tpo -c -o gsnap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gsnap-oligoindex_hr.Tpo .deps/gsnap-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-cellpool.o -MD -MP -MF .deps/gsnap-cellpool.Tpo -c -o gsnap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gsnap-cellpool.Tpo .deps/gsnap-cellpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage2.o -MD -MP -MF .deps/gsnap-stage2.Tpo -c -o gsnap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gsnap-stage2.Tpo .deps/gsnap-stage2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-intron.o -MD -MP -MF .deps/gsnap-intron.Tpo -c -o gsnap-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gsnap-intron.Tpo .deps/gsnap-intron.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-boyer-moore.o -MD -MP -MF .deps/gsnap-boyer-moore.Tpo -c -o gsnap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gsnap-boyer-moore.Tpo .deps/gsnap-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-changepoint.o -MD -MP -MF .deps/gsnap-changepoint.Tpo -c -o gsnap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gsnap-changepoint.Tpo .deps/gsnap-changepoint.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-pbinom.o -MD -MP -MF .deps/gsnap-pbinom.Tpo -c -o gsnap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gsnap-pbinom.Tpo .deps/gsnap-pbinom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-dynprog.o -MD -MP -MF .deps/gsnap-dynprog.Tpo -c -o gsnap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gsnap-dynprog.Tpo .deps/gsnap-dynprog.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gbuffer.o -MD -MP -MF .deps/gsnap-gbuffer.Tpo -c -o gsnap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gsnap-gbuffer.Tpo .deps/gsnap-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-translation.o -MD -MP -MF .deps/gsnap-translation.Tpo -c -o gsnap-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gsnap-translation.Tpo .deps/gsnap-translation.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-doublelist.o -MD -MP -MF .deps/gsnap-doublelist.Tpo -c -o gsnap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gsnap-doublelist.Tpo .deps/gsnap-doublelist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-smooth.o -MD -MP -MF .deps/gsnap-smooth.Tpo -c -o gsnap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gsnap-smooth.Tpo .deps/gsnap-smooth.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-chimera.o -MD -MP -MF .deps/gsnap-chimera.Tpo -c -o gsnap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gsnap-chimera.Tpo .deps/gsnap-chimera.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage3.o -MD -MP -MF .deps/gsnap-stage3.Tpo -c -o gsnap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gsnap-stage3.Tpo .deps/gsnap-stage3.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicestringpool.o -MD -MP -MF .deps/gsnap-splicestringpool.Tpo -c -o gsnap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gsnap-splicestringpool.Tpo .deps/gsnap-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie_build.o -MD -MP -MF .deps/gsnap-splicetrie_build.Tpo -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gsnap-splicetrie_build.Tpo .deps/gsnap-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splicetrie.o -MD -MP -MF .deps/gsnap-splicetrie.Tpo -c -o gsnap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gsnap-splicetrie.Tpo .deps/gsnap-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-splice.o -MD -MP -MF .deps/gsnap-splice.Tpo -c -o gsnap-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/gsnap-splice.Tpo .deps/gsnap-splice.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-indel.o -MD -MP -MF .deps/gsnap-indel.Tpo -c -o gsnap-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/gsnap-indel.Tpo .deps/gsnap-indel.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-bitpack64-access.o -MD -MP -MF .deps/gsnap-bitpack64-access.Tpo -c -o gsnap-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/gsnap-bitpack64-access.Tpo .deps/gsnap-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-sarray-read.o -MD -MP -MF .deps/gsnap-sarray-read.Tpo -c -o gsnap-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c mv -f .deps/gsnap-sarray-read.Tpo .deps/gsnap-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-stage1hr.o -MD -MP -MF .deps/gsnap-stage1hr.Tpo -c -o gsnap-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c mv -f .deps/gsnap-stage1hr.Tpo .deps/gsnap-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-request.o -MD -MP -MF .deps/gsnap-request.Tpo -c -o gsnap-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gsnap-request.Tpo .deps/gsnap-request.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-resulthr.o -MD -MP -MF .deps/gsnap-resulthr.Tpo -c -o gsnap-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/gsnap-resulthr.Tpo .deps/gsnap-resulthr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-inbuffer.o -MD -MP -MF .deps/gsnap-inbuffer.Tpo -c -o gsnap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gsnap-inbuffer.Tpo .deps/gsnap-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-samheader.o -MD -MP -MF .deps/gsnap-samheader.Tpo -c -o gsnap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gsnap-samheader.Tpo .deps/gsnap-samheader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-outbuffer.o -MD -MP -MF .deps/gsnap-outbuffer.Tpo -c -o gsnap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gsnap-outbuffer.Tpo .deps/gsnap-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-datadir.o -MD -MP -MF .deps/gsnap-datadir.Tpo -c -o gsnap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gsnap-datadir.Tpo .deps/gsnap-datadir.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt.o -MD -MP -MF .deps/gsnap-getopt.Tpo -c -o gsnap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gsnap-getopt.Tpo .deps/gsnap-getopt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-getopt1.o -MD -MP -MF .deps/gsnap-getopt1.Tpo -c -o gsnap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gsnap-getopt1.Tpo .deps/gsnap-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT gsnap-gsnap.o -MD -MP -MF .deps/gsnap-gsnap.Tpo -c -o gsnap-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c mv -f .deps/gsnap-gsnap.Tpo .deps/gsnap-gsnap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lbz2 -lm libtool: link: gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o gsnap gsnap-except.o gsnap-assert.o gsnap-mem.o gsnap-intlist.o gsnap-list.o gsnap-littleendian.o gsnap-bigendian.o gsnap-univinterval.o gsnap-interval.o gsnap-uintlist.o gsnap-stopwatch.o gsnap-access.o gsnap-iit-read-univ.o gsnap-iit-read.o gsnap-md5.o gsnap-bzip2.o gsnap-sequence.o gsnap-reader.o gsnap-genomicpos.o gsnap-compress.o gsnap-genome.o gsnap-genome_hr.o gsnap-genome_sites.o gsnap-bitpack64-read.o gsnap-indexdb.o gsnap-indexdb_hr.o gsnap-oligo.o gsnap-chrom.o gsnap-segmentpos.o gsnap-chrnum.o gsnap-maxent_hr.o gsnap-samprint.o gsnap-mapq.o gsnap-shortread.o gsnap-substring.o gsnap-stage3hr.o gsnap-goby.o gsnap-spanningelt.o gsnap-cmet.o gsnap-atoi.o gsnap-maxent.o gsnap-pair.o gsnap-pairpool.o gsnap-diag.o gsnap-diagpool.o gsnap-orderstat.o gsnap-oligoindex_hr.o gsnap-cellpool.o gsnap-stage2.o gsnap-intron.o gsnap-boyer-moore.o gsnap-changepoint.o gsnap-pbinom.o gsnap-dynprog.o gsnap-gbuffer.o gsnap-translation.o gsnap-doublelist.o gsnap-smooth.o gsnap-chimera.o gsnap-stage3.o gsnap-splicestringpool.o gsnap-splicetrie_build.o gsnap-splicetrie.o gsnap-splice.o gsnap-indel.o gsnap-bitpack64-access.o gsnap-sarray-read.o gsnap-stage1hr.o gsnap-request.o gsnap-resulthr.o gsnap-inbuffer.o gsnap-samheader.o gsnap-outbuffer.o gsnap-datadir.o gsnap-getopt.o gsnap-getopt1.o gsnap-gsnap.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-except.o -MD -MP -MF .deps/gsnapl-except.Tpo -c -o gsnapl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/gsnapl-except.Tpo .deps/gsnapl-except.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-assert.o -MD -MP -MF .deps/gsnapl-assert.Tpo -c -o gsnapl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/gsnapl-assert.Tpo .deps/gsnapl-assert.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mem.o -MD -MP -MF .deps/gsnapl-mem.Tpo -c -o gsnapl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/gsnapl-mem.Tpo .deps/gsnapl-mem.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intlist.o -MD -MP -MF .deps/gsnapl-intlist.Tpo -c -o gsnapl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/gsnapl-intlist.Tpo .deps/gsnapl-intlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-list.o -MD -MP -MF .deps/gsnapl-list.Tpo -c -o gsnapl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/gsnapl-list.Tpo .deps/gsnapl-list.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-littleendian.o -MD -MP -MF .deps/gsnapl-littleendian.Tpo -c -o gsnapl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/gsnapl-littleendian.Tpo .deps/gsnapl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bigendian.o -MD -MP -MF .deps/gsnapl-bigendian.Tpo -c -o gsnapl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/gsnapl-bigendian.Tpo .deps/gsnapl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-univinterval.o -MD -MP -MF .deps/gsnapl-univinterval.Tpo -c -o gsnapl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/gsnapl-univinterval.Tpo .deps/gsnapl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-interval.o -MD -MP -MF .deps/gsnapl-interval.Tpo -c -o gsnapl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/gsnapl-interval.Tpo .deps/gsnapl-interval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uintlist.o -MD -MP -MF .deps/gsnapl-uintlist.Tpo -c -o gsnapl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/gsnapl-uintlist.Tpo .deps/gsnapl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-uint8list.o -MD -MP -MF .deps/gsnapl-uint8list.Tpo -c -o gsnapl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c mv -f .deps/gsnapl-uint8list.Tpo .deps/gsnapl-uint8list.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stopwatch.o -MD -MP -MF .deps/gsnapl-stopwatch.Tpo -c -o gsnapl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/gsnapl-stopwatch.Tpo .deps/gsnapl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-access.o -MD -MP -MF .deps/gsnapl-access.Tpo -c -o gsnapl-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/gsnapl-access.Tpo .deps/gsnapl-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read-univ.o -MD -MP -MF .deps/gsnapl-iit-read-univ.Tpo -c -o gsnapl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/gsnapl-iit-read-univ.Tpo .deps/gsnapl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-iit-read.o -MD -MP -MF .deps/gsnapl-iit-read.Tpo -c -o gsnapl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/gsnapl-iit-read.Tpo .deps/gsnapl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-md5.o -MD -MP -MF .deps/gsnapl-md5.Tpo -c -o gsnapl-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/gsnapl-md5.Tpo .deps/gsnapl-md5.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bzip2.o -MD -MP -MF .deps/gsnapl-bzip2.Tpo -c -o gsnapl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/gsnapl-bzip2.Tpo .deps/gsnapl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sequence.o -MD -MP -MF .deps/gsnapl-sequence.Tpo -c -o gsnapl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/gsnapl-sequence.Tpo .deps/gsnapl-sequence.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-reader.o -MD -MP -MF .deps/gsnapl-reader.Tpo -c -o gsnapl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/gsnapl-reader.Tpo .deps/gsnapl-reader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genomicpos.o -MD -MP -MF .deps/gsnapl-genomicpos.Tpo -c -o gsnapl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/gsnapl-genomicpos.Tpo .deps/gsnapl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-compress.o -MD -MP -MF .deps/gsnapl-compress.Tpo -c -o gsnapl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/gsnapl-compress.Tpo .deps/gsnapl-compress.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome.o -MD -MP -MF .deps/gsnapl-genome.Tpo -c -o gsnapl-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/gsnapl-genome.Tpo .deps/gsnapl-genome.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_hr.o -MD -MP -MF .deps/gsnapl-genome_hr.Tpo -c -o gsnapl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/gsnapl-genome_hr.Tpo .deps/gsnapl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-genome_sites.o -MD -MP -MF .deps/gsnapl-genome_sites.Tpo -c -o gsnapl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/gsnapl-genome_sites.Tpo .deps/gsnapl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-read.o -MD -MP -MF .deps/gsnapl-bitpack64-read.Tpo -c -o gsnapl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/gsnapl-bitpack64-read.Tpo .deps/gsnapl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb.o -MD -MP -MF .deps/gsnapl-indexdb.Tpo -c -o gsnapl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/gsnapl-indexdb.Tpo .deps/gsnapl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indexdb_hr.o -MD -MP -MF .deps/gsnapl-indexdb_hr.Tpo -c -o gsnapl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/gsnapl-indexdb_hr.Tpo .deps/gsnapl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligo.o -MD -MP -MF .deps/gsnapl-oligo.Tpo -c -o gsnapl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/gsnapl-oligo.Tpo .deps/gsnapl-oligo.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrom.o -MD -MP -MF .deps/gsnapl-chrom.Tpo -c -o gsnapl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/gsnapl-chrom.Tpo .deps/gsnapl-chrom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-segmentpos.o -MD -MP -MF .deps/gsnapl-segmentpos.Tpo -c -o gsnapl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/gsnapl-segmentpos.Tpo .deps/gsnapl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chrnum.o -MD -MP -MF .deps/gsnapl-chrnum.Tpo -c -o gsnapl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/gsnapl-chrnum.Tpo .deps/gsnapl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent_hr.o -MD -MP -MF .deps/gsnapl-maxent_hr.Tpo -c -o gsnapl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/gsnapl-maxent_hr.Tpo .deps/gsnapl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samprint.o -MD -MP -MF .deps/gsnapl-samprint.Tpo -c -o gsnapl-samprint.o `test -f 'samprint.c' || echo './'`samprint.c mv -f .deps/gsnapl-samprint.Tpo .deps/gsnapl-samprint.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-mapq.o -MD -MP -MF .deps/gsnapl-mapq.Tpo -c -o gsnapl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/gsnapl-mapq.Tpo .deps/gsnapl-mapq.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-shortread.o -MD -MP -MF .deps/gsnapl-shortread.Tpo -c -o gsnapl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/gsnapl-shortread.Tpo .deps/gsnapl-shortread.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-substring.o -MD -MP -MF .deps/gsnapl-substring.Tpo -c -o gsnapl-substring.o `test -f 'substring.c' || echo './'`substring.c mv -f .deps/gsnapl-substring.Tpo .deps/gsnapl-substring.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3hr.o -MD -MP -MF .deps/gsnapl-stage3hr.Tpo -c -o gsnapl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/gsnapl-stage3hr.Tpo .deps/gsnapl-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-goby.o -MD -MP -MF .deps/gsnapl-goby.Tpo -c -o gsnapl-goby.o `test -f 'goby.c' || echo './'`goby.c mv -f .deps/gsnapl-goby.Tpo .deps/gsnapl-goby.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-spanningelt.o -MD -MP -MF .deps/gsnapl-spanningelt.Tpo -c -o gsnapl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/gsnapl-spanningelt.Tpo .deps/gsnapl-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cmet.o -MD -MP -MF .deps/gsnapl-cmet.Tpo -c -o gsnapl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/gsnapl-cmet.Tpo .deps/gsnapl-cmet.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-atoi.o -MD -MP -MF .deps/gsnapl-atoi.Tpo -c -o gsnapl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/gsnapl-atoi.Tpo .deps/gsnapl-atoi.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-maxent.o -MD -MP -MF .deps/gsnapl-maxent.Tpo -c -o gsnapl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/gsnapl-maxent.Tpo .deps/gsnapl-maxent.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pair.o -MD -MP -MF .deps/gsnapl-pair.Tpo -c -o gsnapl-pair.o `test -f 'pair.c' || echo './'`pair.c mv -f .deps/gsnapl-pair.Tpo .deps/gsnapl-pair.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pairpool.o -MD -MP -MF .deps/gsnapl-pairpool.Tpo -c -o gsnapl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/gsnapl-pairpool.Tpo .deps/gsnapl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diag.o -MD -MP -MF .deps/gsnapl-diag.Tpo -c -o gsnapl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/gsnapl-diag.Tpo .deps/gsnapl-diag.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-diagpool.o -MD -MP -MF .deps/gsnapl-diagpool.Tpo -c -o gsnapl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/gsnapl-diagpool.Tpo .deps/gsnapl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-orderstat.o -MD -MP -MF .deps/gsnapl-orderstat.Tpo -c -o gsnapl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/gsnapl-orderstat.Tpo .deps/gsnapl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-oligoindex_hr.o -MD -MP -MF .deps/gsnapl-oligoindex_hr.Tpo -c -o gsnapl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/gsnapl-oligoindex_hr.Tpo .deps/gsnapl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-cellpool.o -MD -MP -MF .deps/gsnapl-cellpool.Tpo -c -o gsnapl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/gsnapl-cellpool.Tpo .deps/gsnapl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage2.o -MD -MP -MF .deps/gsnapl-stage2.Tpo -c -o gsnapl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/gsnapl-stage2.Tpo .deps/gsnapl-stage2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-intron.o -MD -MP -MF .deps/gsnapl-intron.Tpo -c -o gsnapl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/gsnapl-intron.Tpo .deps/gsnapl-intron.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-boyer-moore.o -MD -MP -MF .deps/gsnapl-boyer-moore.Tpo -c -o gsnapl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/gsnapl-boyer-moore.Tpo .deps/gsnapl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-changepoint.o -MD -MP -MF .deps/gsnapl-changepoint.Tpo -c -o gsnapl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/gsnapl-changepoint.Tpo .deps/gsnapl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-pbinom.o -MD -MP -MF .deps/gsnapl-pbinom.Tpo -c -o gsnapl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/gsnapl-pbinom.Tpo .deps/gsnapl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-dynprog.o -MD -MP -MF .deps/gsnapl-dynprog.Tpo -c -o gsnapl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/gsnapl-dynprog.Tpo .deps/gsnapl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gbuffer.o -MD -MP -MF .deps/gsnapl-gbuffer.Tpo -c -o gsnapl-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c mv -f .deps/gsnapl-gbuffer.Tpo .deps/gsnapl-gbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-translation.o -MD -MP -MF .deps/gsnapl-translation.Tpo -c -o gsnapl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/gsnapl-translation.Tpo .deps/gsnapl-translation.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-doublelist.o -MD -MP -MF .deps/gsnapl-doublelist.Tpo -c -o gsnapl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/gsnapl-doublelist.Tpo .deps/gsnapl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-smooth.o -MD -MP -MF .deps/gsnapl-smooth.Tpo -c -o gsnapl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/gsnapl-smooth.Tpo .deps/gsnapl-smooth.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-chimera.o -MD -MP -MF .deps/gsnapl-chimera.Tpo -c -o gsnapl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/gsnapl-chimera.Tpo .deps/gsnapl-chimera.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage3.o -MD -MP -MF .deps/gsnapl-stage3.Tpo -c -o gsnapl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/gsnapl-stage3.Tpo .deps/gsnapl-stage3.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicestringpool.o -MD -MP -MF .deps/gsnapl-splicestringpool.Tpo -c -o gsnapl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/gsnapl-splicestringpool.Tpo .deps/gsnapl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie_build.o -MD -MP -MF .deps/gsnapl-splicetrie_build.Tpo -c -o gsnapl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/gsnapl-splicetrie_build.Tpo .deps/gsnapl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splicetrie.o -MD -MP -MF .deps/gsnapl-splicetrie.Tpo -c -o gsnapl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/gsnapl-splicetrie.Tpo .deps/gsnapl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-splice.o -MD -MP -MF .deps/gsnapl-splice.Tpo -c -o gsnapl-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/gsnapl-splice.Tpo .deps/gsnapl-splice.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-indel.o -MD -MP -MF .deps/gsnapl-indel.Tpo -c -o gsnapl-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/gsnapl-indel.Tpo .deps/gsnapl-indel.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-bitpack64-access.o -MD -MP -MF .deps/gsnapl-bitpack64-access.Tpo -c -o gsnapl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/gsnapl-bitpack64-access.Tpo .deps/gsnapl-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-sarray-read.o -MD -MP -MF .deps/gsnapl-sarray-read.Tpo -c -o gsnapl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c sarray-read.c: In function ‘Sarray_new’: sarray-read.c:302:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 302 | new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); | ^ sarray-read.c:368:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 368 | new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2, | ^ sarray-read.c:434:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 434 | new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T), | ^ sarray-read.c:526:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 526 | new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); | ^ sarray-read.c:653:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 653 | new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len, | ^ sarray-read.c: In function ‘collect_elt_matches’: sarray-read.c:2170:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types] 2170 | array = Uintlist_to_array(&n,difflist); | ^ sarray-read.c:2442:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2442 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2442:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2442 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:2456:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2456 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:64: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:2499:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2499 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2499:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2499 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:2513:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2513 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:35: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:2643:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2643 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2643:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2643 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:2656:113: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2656 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:64: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:2699:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2699 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2699:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2699 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:2712:89: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2712 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:35: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:2752:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types] 2752 | array = Uintlist_to_array(&n,difflist); | ^ sarray-read.c:3024:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3024 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3024:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3024 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:3038:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3038 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:64: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:3082:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3082 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3082:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3082 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:3096:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3096 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:35: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:3217:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3217 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3217:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3217 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:3231:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3231 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:64: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:3274:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3274 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3274:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3274 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:3288:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3288 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:35: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ mv -f .deps/gsnapl-sarray-read.Tpo .deps/gsnapl-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-stage1hr.o -MD -MP -MF .deps/gsnapl-stage1hr.Tpo -c -o gsnapl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c mv -f .deps/gsnapl-stage1hr.Tpo .deps/gsnapl-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-request.o -MD -MP -MF .deps/gsnapl-request.Tpo -c -o gsnapl-request.o `test -f 'request.c' || echo './'`request.c mv -f .deps/gsnapl-request.Tpo .deps/gsnapl-request.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-resulthr.o -MD -MP -MF .deps/gsnapl-resulthr.Tpo -c -o gsnapl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/gsnapl-resulthr.Tpo .deps/gsnapl-resulthr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-inbuffer.o -MD -MP -MF .deps/gsnapl-inbuffer.Tpo -c -o gsnapl-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c mv -f .deps/gsnapl-inbuffer.Tpo .deps/gsnapl-inbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-samheader.o -MD -MP -MF .deps/gsnapl-samheader.Tpo -c -o gsnapl-samheader.o `test -f 'samheader.c' || echo './'`samheader.c mv -f .deps/gsnapl-samheader.Tpo .deps/gsnapl-samheader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-outbuffer.o -MD -MP -MF .deps/gsnapl-outbuffer.Tpo -c -o gsnapl-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c mv -f .deps/gsnapl-outbuffer.Tpo .deps/gsnapl-outbuffer.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-datadir.o -MD -MP -MF .deps/gsnapl-datadir.Tpo -c -o gsnapl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/gsnapl-datadir.Tpo .deps/gsnapl-datadir.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt.o -MD -MP -MF .deps/gsnapl-getopt.Tpo -c -o gsnapl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/gsnapl-getopt.Tpo .deps/gsnapl-getopt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-getopt1.o -MD -MP -MF .deps/gsnapl-getopt1.Tpo -c -o gsnapl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/gsnapl-getopt1.Tpo .deps/gsnapl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT gsnapl-gsnap.o -MD -MP -MF .deps/gsnapl-gsnap.Tpo -c -o gsnapl-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c mv -f .deps/gsnapl-gsnap.Tpo .deps/gsnapl-gsnap.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lz -lbz2 -lm libtool: link: gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o gsnapl gsnapl-except.o gsnapl-assert.o gsnapl-mem.o gsnapl-intlist.o gsnapl-list.o gsnapl-littleendian.o gsnapl-bigendian.o gsnapl-univinterval.o gsnapl-interval.o gsnapl-uintlist.o gsnapl-uint8list.o gsnapl-stopwatch.o gsnapl-access.o gsnapl-iit-read-univ.o gsnapl-iit-read.o gsnapl-md5.o gsnapl-bzip2.o gsnapl-sequence.o gsnapl-reader.o gsnapl-genomicpos.o gsnapl-compress.o gsnapl-genome.o gsnapl-genome_hr.o gsnapl-genome_sites.o gsnapl-bitpack64-read.o gsnapl-indexdb.o gsnapl-indexdb_hr.o gsnapl-oligo.o gsnapl-chrom.o gsnapl-segmentpos.o gsnapl-chrnum.o gsnapl-maxent_hr.o gsnapl-samprint.o gsnapl-mapq.o gsnapl-shortread.o gsnapl-substring.o gsnapl-stage3hr.o gsnapl-goby.o gsnapl-spanningelt.o gsnapl-cmet.o gsnapl-atoi.o gsnapl-maxent.o gsnapl-pair.o gsnapl-pairpool.o gsnapl-diag.o gsnapl-diagpool.o gsnapl-orderstat.o gsnapl-oligoindex_hr.o gsnapl-cellpool.o gsnapl-stage2.o gsnapl-intron.o gsnapl-boyer-moore.o gsnapl-changepoint.o gsnapl-pbinom.o gsnapl-dynprog.o gsnapl-gbuffer.o gsnapl-translation.o gsnapl-doublelist.o gsnapl-smooth.o gsnapl-chimera.o gsnapl-stage3.o gsnapl-splicestringpool.o gsnapl-splicetrie_build.o gsnapl-splicetrie.o gsnapl-splice.o gsnapl-indel.o gsnapl-bitpack64-access.o gsnapl-sarray-read.o gsnapl-stage1hr.o gsnapl-request.o gsnapl-resulthr.o gsnapl-inbuffer.o gsnapl-samheader.o gsnapl-outbuffer.o gsnapl-datadir.o gsnapl-getopt.o gsnapl-getopt1.o gsnapl-gsnap.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-except.o -MD -MP -MF .deps/uniqscan-except.Tpo -c -o uniqscan-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/uniqscan-except.Tpo .deps/uniqscan-except.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-assert.o -MD -MP -MF .deps/uniqscan-assert.Tpo -c -o uniqscan-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/uniqscan-assert.Tpo .deps/uniqscan-assert.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mem.o -MD -MP -MF .deps/uniqscan-mem.Tpo -c -o uniqscan-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/uniqscan-mem.Tpo .deps/uniqscan-mem.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intlist.o -MD -MP -MF .deps/uniqscan-intlist.Tpo -c -o uniqscan-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/uniqscan-intlist.Tpo .deps/uniqscan-intlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-list.o -MD -MP -MF .deps/uniqscan-list.Tpo -c -o uniqscan-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/uniqscan-list.Tpo .deps/uniqscan-list.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-littleendian.o -MD -MP -MF .deps/uniqscan-littleendian.Tpo -c -o uniqscan-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/uniqscan-littleendian.Tpo .deps/uniqscan-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bigendian.o -MD -MP -MF .deps/uniqscan-bigendian.Tpo -c -o uniqscan-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/uniqscan-bigendian.Tpo .deps/uniqscan-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-univinterval.o -MD -MP -MF .deps/uniqscan-univinterval.Tpo -c -o uniqscan-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/uniqscan-univinterval.Tpo .deps/uniqscan-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-interval.o -MD -MP -MF .deps/uniqscan-interval.Tpo -c -o uniqscan-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/uniqscan-interval.Tpo .deps/uniqscan-interval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uintlist.o -MD -MP -MF .deps/uniqscan-uintlist.Tpo -c -o uniqscan-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/uniqscan-uintlist.Tpo .deps/uniqscan-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stopwatch.o -MD -MP -MF .deps/uniqscan-stopwatch.Tpo -c -o uniqscan-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/uniqscan-stopwatch.Tpo .deps/uniqscan-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-access.o -MD -MP -MF .deps/uniqscan-access.Tpo -c -o uniqscan-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/uniqscan-access.Tpo .deps/uniqscan-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read-univ.o -MD -MP -MF .deps/uniqscan-iit-read-univ.Tpo -c -o uniqscan-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/uniqscan-iit-read-univ.Tpo .deps/uniqscan-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-iit-read.o -MD -MP -MF .deps/uniqscan-iit-read.Tpo -c -o uniqscan-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/uniqscan-iit-read.Tpo .deps/uniqscan-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-md5.o -MD -MP -MF .deps/uniqscan-md5.Tpo -c -o uniqscan-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/uniqscan-md5.Tpo .deps/uniqscan-md5.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bzip2.o -MD -MP -MF .deps/uniqscan-bzip2.Tpo -c -o uniqscan-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/uniqscan-bzip2.Tpo .deps/uniqscan-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sequence.o -MD -MP -MF .deps/uniqscan-sequence.Tpo -c -o uniqscan-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/uniqscan-sequence.Tpo .deps/uniqscan-sequence.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-reader.o -MD -MP -MF .deps/uniqscan-reader.Tpo -c -o uniqscan-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/uniqscan-reader.Tpo .deps/uniqscan-reader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genomicpos.o -MD -MP -MF .deps/uniqscan-genomicpos.Tpo -c -o uniqscan-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/uniqscan-genomicpos.Tpo .deps/uniqscan-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-compress.o -MD -MP -MF .deps/uniqscan-compress.Tpo -c -o uniqscan-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/uniqscan-compress.Tpo .deps/uniqscan-compress.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome.o -MD -MP -MF .deps/uniqscan-genome.Tpo -c -o uniqscan-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/uniqscan-genome.Tpo .deps/uniqscan-genome.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_hr.o -MD -MP -MF .deps/uniqscan-genome_hr.Tpo -c -o uniqscan-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/uniqscan-genome_hr.Tpo .deps/uniqscan-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-genome_sites.o -MD -MP -MF .deps/uniqscan-genome_sites.Tpo -c -o uniqscan-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/uniqscan-genome_sites.Tpo .deps/uniqscan-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-read.o -MD -MP -MF .deps/uniqscan-bitpack64-read.Tpo -c -o uniqscan-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/uniqscan-bitpack64-read.Tpo .deps/uniqscan-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb.o -MD -MP -MF .deps/uniqscan-indexdb.Tpo -c -o uniqscan-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/uniqscan-indexdb.Tpo .deps/uniqscan-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indexdb_hr.o -MD -MP -MF .deps/uniqscan-indexdb_hr.Tpo -c -o uniqscan-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/uniqscan-indexdb_hr.Tpo .deps/uniqscan-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligo.o -MD -MP -MF .deps/uniqscan-oligo.Tpo -c -o uniqscan-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/uniqscan-oligo.Tpo .deps/uniqscan-oligo.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrom.o -MD -MP -MF .deps/uniqscan-chrom.Tpo -c -o uniqscan-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/uniqscan-chrom.Tpo .deps/uniqscan-chrom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-segmentpos.o -MD -MP -MF .deps/uniqscan-segmentpos.Tpo -c -o uniqscan-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/uniqscan-segmentpos.Tpo .deps/uniqscan-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chrnum.o -MD -MP -MF .deps/uniqscan-chrnum.Tpo -c -o uniqscan-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/uniqscan-chrnum.Tpo .deps/uniqscan-chrnum.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent_hr.o -MD -MP -MF .deps/uniqscan-maxent_hr.Tpo -c -o uniqscan-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/uniqscan-maxent_hr.Tpo .deps/uniqscan-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-mapq.o -MD -MP -MF .deps/uniqscan-mapq.Tpo -c -o uniqscan-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/uniqscan-mapq.Tpo .deps/uniqscan-mapq.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-shortread.o -MD -MP -MF .deps/uniqscan-shortread.Tpo -c -o uniqscan-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/uniqscan-shortread.Tpo .deps/uniqscan-shortread.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-substring.o -MD -MP -MF .deps/uniqscan-substring.Tpo -c -o uniqscan-substring.o `test -f 'substring.c' || echo './'`substring.c mv -f .deps/uniqscan-substring.Tpo .deps/uniqscan-substring.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3hr.o -MD -MP -MF .deps/uniqscan-stage3hr.Tpo -c -o uniqscan-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/uniqscan-stage3hr.Tpo .deps/uniqscan-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-spanningelt.o -MD -MP -MF .deps/uniqscan-spanningelt.Tpo -c -o uniqscan-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/uniqscan-spanningelt.Tpo .deps/uniqscan-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cmet.o -MD -MP -MF .deps/uniqscan-cmet.Tpo -c -o uniqscan-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/uniqscan-cmet.Tpo .deps/uniqscan-cmet.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-atoi.o -MD -MP -MF .deps/uniqscan-atoi.Tpo -c -o uniqscan-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/uniqscan-atoi.Tpo .deps/uniqscan-atoi.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-maxent.o -MD -MP -MF .deps/uniqscan-maxent.Tpo -c -o uniqscan-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/uniqscan-maxent.Tpo .deps/uniqscan-maxent.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pair.o -MD -MP -MF .deps/uniqscan-pair.Tpo -c -o uniqscan-pair.o `test -f 'pair.c' || echo './'`pair.c mv -f .deps/uniqscan-pair.Tpo .deps/uniqscan-pair.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pairpool.o -MD -MP -MF .deps/uniqscan-pairpool.Tpo -c -o uniqscan-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/uniqscan-pairpool.Tpo .deps/uniqscan-pairpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diag.o -MD -MP -MF .deps/uniqscan-diag.Tpo -c -o uniqscan-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/uniqscan-diag.Tpo .deps/uniqscan-diag.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-diagpool.o -MD -MP -MF .deps/uniqscan-diagpool.Tpo -c -o uniqscan-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/uniqscan-diagpool.Tpo .deps/uniqscan-diagpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-orderstat.o -MD -MP -MF .deps/uniqscan-orderstat.Tpo -c -o uniqscan-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/uniqscan-orderstat.Tpo .deps/uniqscan-orderstat.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-oligoindex_hr.o -MD -MP -MF .deps/uniqscan-oligoindex_hr.Tpo -c -o uniqscan-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/uniqscan-oligoindex_hr.Tpo .deps/uniqscan-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-cellpool.o -MD -MP -MF .deps/uniqscan-cellpool.Tpo -c -o uniqscan-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/uniqscan-cellpool.Tpo .deps/uniqscan-cellpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage2.o -MD -MP -MF .deps/uniqscan-stage2.Tpo -c -o uniqscan-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/uniqscan-stage2.Tpo .deps/uniqscan-stage2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-intron.o -MD -MP -MF .deps/uniqscan-intron.Tpo -c -o uniqscan-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/uniqscan-intron.Tpo .deps/uniqscan-intron.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-boyer-moore.o -MD -MP -MF .deps/uniqscan-boyer-moore.Tpo -c -o uniqscan-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/uniqscan-boyer-moore.Tpo .deps/uniqscan-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-changepoint.o -MD -MP -MF .deps/uniqscan-changepoint.Tpo -c -o uniqscan-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/uniqscan-changepoint.Tpo .deps/uniqscan-changepoint.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-pbinom.o -MD -MP -MF .deps/uniqscan-pbinom.Tpo -c -o uniqscan-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/uniqscan-pbinom.Tpo .deps/uniqscan-pbinom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-dynprog.o -MD -MP -MF .deps/uniqscan-dynprog.Tpo -c -o uniqscan-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/uniqscan-dynprog.Tpo .deps/uniqscan-dynprog.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-translation.o -MD -MP -MF .deps/uniqscan-translation.Tpo -c -o uniqscan-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/uniqscan-translation.Tpo .deps/uniqscan-translation.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-doublelist.o -MD -MP -MF .deps/uniqscan-doublelist.Tpo -c -o uniqscan-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/uniqscan-doublelist.Tpo .deps/uniqscan-doublelist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-smooth.o -MD -MP -MF .deps/uniqscan-smooth.Tpo -c -o uniqscan-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/uniqscan-smooth.Tpo .deps/uniqscan-smooth.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-chimera.o -MD -MP -MF .deps/uniqscan-chimera.Tpo -c -o uniqscan-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/uniqscan-chimera.Tpo .deps/uniqscan-chimera.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage3.o -MD -MP -MF .deps/uniqscan-stage3.Tpo -c -o uniqscan-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/uniqscan-stage3.Tpo .deps/uniqscan-stage3.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicestringpool.o -MD -MP -MF .deps/uniqscan-splicestringpool.Tpo -c -o uniqscan-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/uniqscan-splicestringpool.Tpo .deps/uniqscan-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie_build.o -MD -MP -MF .deps/uniqscan-splicetrie_build.Tpo -c -o uniqscan-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/uniqscan-splicetrie_build.Tpo .deps/uniqscan-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splicetrie.o -MD -MP -MF .deps/uniqscan-splicetrie.Tpo -c -o uniqscan-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/uniqscan-splicetrie.Tpo .deps/uniqscan-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-splice.o -MD -MP -MF .deps/uniqscan-splice.Tpo -c -o uniqscan-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/uniqscan-splice.Tpo .deps/uniqscan-splice.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-indel.o -MD -MP -MF .deps/uniqscan-indel.Tpo -c -o uniqscan-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/uniqscan-indel.Tpo .deps/uniqscan-indel.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-bitpack64-access.o -MD -MP -MF .deps/uniqscan-bitpack64-access.Tpo -c -o uniqscan-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/uniqscan-bitpack64-access.Tpo .deps/uniqscan-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-sarray-read.o -MD -MP -MF .deps/uniqscan-sarray-read.Tpo -c -o uniqscan-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c mv -f .deps/uniqscan-sarray-read.Tpo .deps/uniqscan-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-stage1hr.o -MD -MP -MF .deps/uniqscan-stage1hr.Tpo -c -o uniqscan-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c mv -f .deps/uniqscan-stage1hr.Tpo .deps/uniqscan-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-resulthr.o -MD -MP -MF .deps/uniqscan-resulthr.Tpo -c -o uniqscan-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/uniqscan-resulthr.Tpo .deps/uniqscan-resulthr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-datadir.o -MD -MP -MF .deps/uniqscan-datadir.Tpo -c -o uniqscan-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/uniqscan-datadir.Tpo .deps/uniqscan-datadir.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt.o -MD -MP -MF .deps/uniqscan-getopt.Tpo -c -o uniqscan-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/uniqscan-getopt.Tpo .deps/uniqscan-getopt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-getopt1.o -MD -MP -MF .deps/uniqscan-getopt1.Tpo -c -o uniqscan-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/uniqscan-getopt1.Tpo .deps/uniqscan-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -MT uniqscan-uniqscan.o -MD -MP -MF .deps/uniqscan-uniqscan.Tpo -c -o uniqscan-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c mv -f .deps/uniqscan-uniqscan.Tpo .deps/uniqscan-uniqscan.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lz -lbz2 -lm libtool: link: gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -O3 -o uniqscan uniqscan-except.o uniqscan-assert.o uniqscan-mem.o uniqscan-intlist.o uniqscan-list.o uniqscan-littleendian.o uniqscan-bigendian.o uniqscan-univinterval.o uniqscan-interval.o uniqscan-uintlist.o uniqscan-stopwatch.o uniqscan-access.o uniqscan-iit-read-univ.o uniqscan-iit-read.o uniqscan-md5.o uniqscan-bzip2.o uniqscan-sequence.o uniqscan-reader.o uniqscan-genomicpos.o uniqscan-compress.o uniqscan-genome.o uniqscan-genome_hr.o uniqscan-genome_sites.o uniqscan-bitpack64-read.o uniqscan-indexdb.o uniqscan-indexdb_hr.o uniqscan-oligo.o uniqscan-chrom.o uniqscan-segmentpos.o uniqscan-chrnum.o uniqscan-maxent_hr.o uniqscan-mapq.o uniqscan-shortread.o uniqscan-substring.o uniqscan-stage3hr.o uniqscan-spanningelt.o uniqscan-cmet.o uniqscan-atoi.o uniqscan-maxent.o uniqscan-pair.o uniqscan-pairpool.o uniqscan-diag.o uniqscan-diagpool.o uniqscan-orderstat.o uniqscan-oligoindex_hr.o uniqscan-cellpool.o uniqscan-stage2.o uniqscan-intron.o uniqscan-boyer-moore.o uniqscan-changepoint.o uniqscan-pbinom.o uniqscan-dynprog.o uniqscan-translation.o uniqscan-doublelist.o uniqscan-smooth.o uniqscan-chimera.o uniqscan-stage3.o uniqscan-splicestringpool.o uniqscan-splicetrie_build.o uniqscan-splicetrie.o uniqscan-splice.o uniqscan-indel.o uniqscan-bitpack64-access.o uniqscan-sarray-read.o uniqscan-stage1hr.o uniqscan-resulthr.o uniqscan-datadir.o uniqscan-getopt.o uniqscan-getopt1.o uniqscan-uniqscan.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-except.o -MD -MP -MF .deps/uniqscanl-except.Tpo -c -o uniqscanl-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/uniqscanl-except.Tpo .deps/uniqscanl-except.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-assert.o -MD -MP -MF .deps/uniqscanl-assert.Tpo -c -o uniqscanl-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/uniqscanl-assert.Tpo .deps/uniqscanl-assert.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mem.o -MD -MP -MF .deps/uniqscanl-mem.Tpo -c -o uniqscanl-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/uniqscanl-mem.Tpo .deps/uniqscanl-mem.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intlist.o -MD -MP -MF .deps/uniqscanl-intlist.Tpo -c -o uniqscanl-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/uniqscanl-intlist.Tpo .deps/uniqscanl-intlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-list.o -MD -MP -MF .deps/uniqscanl-list.Tpo -c -o uniqscanl-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/uniqscanl-list.Tpo .deps/uniqscanl-list.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-littleendian.o -MD -MP -MF .deps/uniqscanl-littleendian.Tpo -c -o uniqscanl-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/uniqscanl-littleendian.Tpo .deps/uniqscanl-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bigendian.o -MD -MP -MF .deps/uniqscanl-bigendian.Tpo -c -o uniqscanl-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/uniqscanl-bigendian.Tpo .deps/uniqscanl-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-univinterval.o -MD -MP -MF .deps/uniqscanl-univinterval.Tpo -c -o uniqscanl-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/uniqscanl-univinterval.Tpo .deps/uniqscanl-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-interval.o -MD -MP -MF .deps/uniqscanl-interval.Tpo -c -o uniqscanl-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/uniqscanl-interval.Tpo .deps/uniqscanl-interval.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uintlist.o -MD -MP -MF .deps/uniqscanl-uintlist.Tpo -c -o uniqscanl-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/uniqscanl-uintlist.Tpo .deps/uniqscanl-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uint8list.o -MD -MP -MF .deps/uniqscanl-uint8list.Tpo -c -o uniqscanl-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c mv -f .deps/uniqscanl-uint8list.Tpo .deps/uniqscanl-uint8list.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stopwatch.o -MD -MP -MF .deps/uniqscanl-stopwatch.Tpo -c -o uniqscanl-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/uniqscanl-stopwatch.Tpo .deps/uniqscanl-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-access.o -MD -MP -MF .deps/uniqscanl-access.Tpo -c -o uniqscanl-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/uniqscanl-access.Tpo .deps/uniqscanl-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read-univ.o -MD -MP -MF .deps/uniqscanl-iit-read-univ.Tpo -c -o uniqscanl-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/uniqscanl-iit-read-univ.Tpo .deps/uniqscanl-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-iit-read.o -MD -MP -MF .deps/uniqscanl-iit-read.Tpo -c -o uniqscanl-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/uniqscanl-iit-read.Tpo .deps/uniqscanl-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-md5.o -MD -MP -MF .deps/uniqscanl-md5.Tpo -c -o uniqscanl-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/uniqscanl-md5.Tpo .deps/uniqscanl-md5.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bzip2.o -MD -MP -MF .deps/uniqscanl-bzip2.Tpo -c -o uniqscanl-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/uniqscanl-bzip2.Tpo .deps/uniqscanl-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sequence.o -MD -MP -MF .deps/uniqscanl-sequence.Tpo -c -o uniqscanl-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/uniqscanl-sequence.Tpo .deps/uniqscanl-sequence.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-reader.o -MD -MP -MF .deps/uniqscanl-reader.Tpo -c -o uniqscanl-reader.o `test -f 'reader.c' || echo './'`reader.c mv -f .deps/uniqscanl-reader.Tpo .deps/uniqscanl-reader.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genomicpos.o -MD -MP -MF .deps/uniqscanl-genomicpos.Tpo -c -o uniqscanl-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/uniqscanl-genomicpos.Tpo .deps/uniqscanl-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-compress.o -MD -MP -MF .deps/uniqscanl-compress.Tpo -c -o uniqscanl-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/uniqscanl-compress.Tpo .deps/uniqscanl-compress.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome.o -MD -MP -MF .deps/uniqscanl-genome.Tpo -c -o uniqscanl-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/uniqscanl-genome.Tpo .deps/uniqscanl-genome.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_hr.o -MD -MP -MF .deps/uniqscanl-genome_hr.Tpo -c -o uniqscanl-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/uniqscanl-genome_hr.Tpo .deps/uniqscanl-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-genome_sites.o -MD -MP -MF .deps/uniqscanl-genome_sites.Tpo -c -o uniqscanl-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c mv -f .deps/uniqscanl-genome_sites.Tpo .deps/uniqscanl-genome_sites.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-read.o -MD -MP -MF .deps/uniqscanl-bitpack64-read.Tpo -c -o uniqscanl-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/uniqscanl-bitpack64-read.Tpo .deps/uniqscanl-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb.o -MD -MP -MF .deps/uniqscanl-indexdb.Tpo -c -o uniqscanl-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/uniqscanl-indexdb.Tpo .deps/uniqscanl-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indexdb_hr.o -MD -MP -MF .deps/uniqscanl-indexdb_hr.Tpo -c -o uniqscanl-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c mv -f .deps/uniqscanl-indexdb_hr.Tpo .deps/uniqscanl-indexdb_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligo.o -MD -MP -MF .deps/uniqscanl-oligo.Tpo -c -o uniqscanl-oligo.o `test -f 'oligo.c' || echo './'`oligo.c mv -f .deps/uniqscanl-oligo.Tpo .deps/uniqscanl-oligo.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrom.o -MD -MP -MF .deps/uniqscanl-chrom.Tpo -c -o uniqscanl-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/uniqscanl-chrom.Tpo .deps/uniqscanl-chrom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-segmentpos.o -MD -MP -MF .deps/uniqscanl-segmentpos.Tpo -c -o uniqscanl-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c mv -f .deps/uniqscanl-segmentpos.Tpo .deps/uniqscanl-segmentpos.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chrnum.o -MD -MP -MF .deps/uniqscanl-chrnum.Tpo -c -o uniqscanl-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c mv -f .deps/uniqscanl-chrnum.Tpo .deps/uniqscanl-chrnum.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent_hr.o -MD -MP -MF .deps/uniqscanl-maxent_hr.Tpo -c -o uniqscanl-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c mv -f .deps/uniqscanl-maxent_hr.Tpo .deps/uniqscanl-maxent_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-mapq.o -MD -MP -MF .deps/uniqscanl-mapq.Tpo -c -o uniqscanl-mapq.o `test -f 'mapq.c' || echo './'`mapq.c mv -f .deps/uniqscanl-mapq.Tpo .deps/uniqscanl-mapq.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-shortread.o -MD -MP -MF .deps/uniqscanl-shortread.Tpo -c -o uniqscanl-shortread.o `test -f 'shortread.c' || echo './'`shortread.c mv -f .deps/uniqscanl-shortread.Tpo .deps/uniqscanl-shortread.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-substring.o -MD -MP -MF .deps/uniqscanl-substring.Tpo -c -o uniqscanl-substring.o `test -f 'substring.c' || echo './'`substring.c mv -f .deps/uniqscanl-substring.Tpo .deps/uniqscanl-substring.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3hr.o -MD -MP -MF .deps/uniqscanl-stage3hr.Tpo -c -o uniqscanl-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c mv -f .deps/uniqscanl-stage3hr.Tpo .deps/uniqscanl-stage3hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-spanningelt.o -MD -MP -MF .deps/uniqscanl-spanningelt.Tpo -c -o uniqscanl-spanningelt.o `test -f 'spanningelt.c' || echo './'`spanningelt.c mv -f .deps/uniqscanl-spanningelt.Tpo .deps/uniqscanl-spanningelt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cmet.o -MD -MP -MF .deps/uniqscanl-cmet.Tpo -c -o uniqscanl-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/uniqscanl-cmet.Tpo .deps/uniqscanl-cmet.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-atoi.o -MD -MP -MF .deps/uniqscanl-atoi.Tpo -c -o uniqscanl-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/uniqscanl-atoi.Tpo .deps/uniqscanl-atoi.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-maxent.o -MD -MP -MF .deps/uniqscanl-maxent.Tpo -c -o uniqscanl-maxent.o `test -f 'maxent.c' || echo './'`maxent.c mv -f .deps/uniqscanl-maxent.Tpo .deps/uniqscanl-maxent.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pair.o -MD -MP -MF .deps/uniqscanl-pair.Tpo -c -o uniqscanl-pair.o `test -f 'pair.c' || echo './'`pair.c mv -f .deps/uniqscanl-pair.Tpo .deps/uniqscanl-pair.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pairpool.o -MD -MP -MF .deps/uniqscanl-pairpool.Tpo -c -o uniqscanl-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c mv -f .deps/uniqscanl-pairpool.Tpo .deps/uniqscanl-pairpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diag.o -MD -MP -MF .deps/uniqscanl-diag.Tpo -c -o uniqscanl-diag.o `test -f 'diag.c' || echo './'`diag.c mv -f .deps/uniqscanl-diag.Tpo .deps/uniqscanl-diag.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-diagpool.o -MD -MP -MF .deps/uniqscanl-diagpool.Tpo -c -o uniqscanl-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c mv -f .deps/uniqscanl-diagpool.Tpo .deps/uniqscanl-diagpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-orderstat.o -MD -MP -MF .deps/uniqscanl-orderstat.Tpo -c -o uniqscanl-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c mv -f .deps/uniqscanl-orderstat.Tpo .deps/uniqscanl-orderstat.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-oligoindex_hr.o -MD -MP -MF .deps/uniqscanl-oligoindex_hr.Tpo -c -o uniqscanl-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c mv -f .deps/uniqscanl-oligoindex_hr.Tpo .deps/uniqscanl-oligoindex_hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-cellpool.o -MD -MP -MF .deps/uniqscanl-cellpool.Tpo -c -o uniqscanl-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c mv -f .deps/uniqscanl-cellpool.Tpo .deps/uniqscanl-cellpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage2.o -MD -MP -MF .deps/uniqscanl-stage2.Tpo -c -o uniqscanl-stage2.o `test -f 'stage2.c' || echo './'`stage2.c mv -f .deps/uniqscanl-stage2.Tpo .deps/uniqscanl-stage2.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-intron.o -MD -MP -MF .deps/uniqscanl-intron.Tpo -c -o uniqscanl-intron.o `test -f 'intron.c' || echo './'`intron.c mv -f .deps/uniqscanl-intron.Tpo .deps/uniqscanl-intron.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-boyer-moore.o -MD -MP -MF .deps/uniqscanl-boyer-moore.Tpo -c -o uniqscanl-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c mv -f .deps/uniqscanl-boyer-moore.Tpo .deps/uniqscanl-boyer-moore.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-changepoint.o -MD -MP -MF .deps/uniqscanl-changepoint.Tpo -c -o uniqscanl-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c mv -f .deps/uniqscanl-changepoint.Tpo .deps/uniqscanl-changepoint.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-pbinom.o -MD -MP -MF .deps/uniqscanl-pbinom.Tpo -c -o uniqscanl-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c mv -f .deps/uniqscanl-pbinom.Tpo .deps/uniqscanl-pbinom.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-dynprog.o -MD -MP -MF .deps/uniqscanl-dynprog.Tpo -c -o uniqscanl-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c mv -f .deps/uniqscanl-dynprog.Tpo .deps/uniqscanl-dynprog.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-translation.o -MD -MP -MF .deps/uniqscanl-translation.Tpo -c -o uniqscanl-translation.o `test -f 'translation.c' || echo './'`translation.c mv -f .deps/uniqscanl-translation.Tpo .deps/uniqscanl-translation.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-doublelist.o -MD -MP -MF .deps/uniqscanl-doublelist.Tpo -c -o uniqscanl-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c mv -f .deps/uniqscanl-doublelist.Tpo .deps/uniqscanl-doublelist.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-smooth.o -MD -MP -MF .deps/uniqscanl-smooth.Tpo -c -o uniqscanl-smooth.o `test -f 'smooth.c' || echo './'`smooth.c mv -f .deps/uniqscanl-smooth.Tpo .deps/uniqscanl-smooth.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-chimera.o -MD -MP -MF .deps/uniqscanl-chimera.Tpo -c -o uniqscanl-chimera.o `test -f 'chimera.c' || echo './'`chimera.c mv -f .deps/uniqscanl-chimera.Tpo .deps/uniqscanl-chimera.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage3.o -MD -MP -MF .deps/uniqscanl-stage3.Tpo -c -o uniqscanl-stage3.o `test -f 'stage3.c' || echo './'`stage3.c mv -f .deps/uniqscanl-stage3.Tpo .deps/uniqscanl-stage3.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicestringpool.o -MD -MP -MF .deps/uniqscanl-splicestringpool.Tpo -c -o uniqscanl-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c mv -f .deps/uniqscanl-splicestringpool.Tpo .deps/uniqscanl-splicestringpool.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie_build.o -MD -MP -MF .deps/uniqscanl-splicetrie_build.Tpo -c -o uniqscanl-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c mv -f .deps/uniqscanl-splicetrie_build.Tpo .deps/uniqscanl-splicetrie_build.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splicetrie.o -MD -MP -MF .deps/uniqscanl-splicetrie.Tpo -c -o uniqscanl-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c mv -f .deps/uniqscanl-splicetrie.Tpo .deps/uniqscanl-splicetrie.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-splice.o -MD -MP -MF .deps/uniqscanl-splice.Tpo -c -o uniqscanl-splice.o `test -f 'splice.c' || echo './'`splice.c mv -f .deps/uniqscanl-splice.Tpo .deps/uniqscanl-splice.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-indel.o -MD -MP -MF .deps/uniqscanl-indel.Tpo -c -o uniqscanl-indel.o `test -f 'indel.c' || echo './'`indel.c mv -f .deps/uniqscanl-indel.Tpo .deps/uniqscanl-indel.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-bitpack64-access.o -MD -MP -MF .deps/uniqscanl-bitpack64-access.Tpo -c -o uniqscanl-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c mv -f .deps/uniqscanl-bitpack64-access.Tpo .deps/uniqscanl-bitpack64-access.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-sarray-read.o -MD -MP -MF .deps/uniqscanl-sarray-read.Tpo -c -o uniqscanl-sarray-read.o `test -f 'sarray-read.c' || echo './'`sarray-read.c sarray-read.c: In function ‘Sarray_new’: sarray-read.c:302:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 302 | new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); | ^ sarray-read.c:368:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 368 | new->lcpcomp = (Univcoord_T *) Access_mmap_and_preload(&new->lcpcomp_fd,&new->lcpcomp_len,&npages,&seconds2, | ^ sarray-read.c:434:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 434 | new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len,filename,sizeof(Univcoord_T), | ^ sarray-read.c:526:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 526 | new->lcpcomp = (Univcoord_T *) Access_allocated(&new->lcpcomp_len,&seconds2,filename,sizeof(Univcoord_T)); | ^ sarray-read.c:653:22: warning: assignment to ‘UINT4 *’ {aka ‘unsigned int *’} from incompatible pointer type ‘Univcoord_T *’ {aka ‘long long unsigned int *’} [-Wincompatible-pointer-types] 653 | new->lcpcomp = (Univcoord_T *) Access_mmap(&new->lcpcomp_fd,&new->lcpcomp_len, | ^ sarray-read.c: In function ‘collect_elt_matches’: sarray-read.c:2170:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types] 2170 | array = Uintlist_to_array(&n,difflist); | ^ sarray-read.c:2442:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2442 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from genomicpos.h:9, from genome.h:8, from sarray-read.h:5, from sarray-read.c:9: uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2442:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2442 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:2456:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2456 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} In file included from sarray-read.c:24: stage3hr.h:296:64: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:2499:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2499 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2499:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2499 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:2513:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2513 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:35: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:2643:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2643 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2643:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2643 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:2656:113: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2656 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:64: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:2699:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 2699 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:2699:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 2699 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:2712:89: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 2712 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:35: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:2752:11: warning: assignment to ‘Univcoord_T *’ {aka ‘long long unsigned int *’} from incompatible pointer type ‘UINT4 *’ {aka ‘unsigned int *’} [-Wincompatible-pointer-types] 2752 | array = Uintlist_to_array(&n,difflist); | ^ sarray-read.c:3024:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3024 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3024:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3024 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:3038:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3038 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:64: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:3082:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3082 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3082:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3082 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:3096:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3096 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:35: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ sarray-read.c:3217:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3217 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3217:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3217 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(acceptor)); | ^ sarray-read.c:3231:97: warning: passing argument 12 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3231 | /*ambcoords_donor*/NULL,ambcoords, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:64: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ sarray-read.c:3274:44: warning: passing argument 1 of ‘Uint8list_push’ from incompatible pointer type [-Wincompatible-pointer-types] 3274 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} uint8list.h:11:19: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 11 | Uint8list_push (T list, UINT8 x); | ^ sarray-read.c:3274:27: warning: assignment to ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} from incompatible pointer type ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} [-Wincompatible-pointer-types] 3274 | ambcoords = Uint8list_push(ambcoords,Substring_splicecoord(donor)); | ^ sarray-read.c:3288:73: warning: passing argument 11 of ‘Stage3end_new_splice’ from incompatible pointer type [-Wincompatible-pointer-types] 3288 | ambcoords,/*ambcoords_acceptor*/NULL, | ^~~~~~~~~ | | | Uintlist_T {aka struct Uintlist_T *} stage3hr.h:296:35: note: expected ‘Uint8list_T’ {aka ‘struct Uint8list_T *’} but argument is of type ‘Uintlist_T’ {aka ‘struct Uintlist_T *’} 296 | Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ mv -f .deps/uniqscanl-sarray-read.Tpo .deps/uniqscanl-sarray-read.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-stage1hr.o -MD -MP -MF .deps/uniqscanl-stage1hr.Tpo -c -o uniqscanl-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c mv -f .deps/uniqscanl-stage1hr.Tpo .deps/uniqscanl-stage1hr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-resulthr.o -MD -MP -MF .deps/uniqscanl-resulthr.Tpo -c -o uniqscanl-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c mv -f .deps/uniqscanl-resulthr.Tpo .deps/uniqscanl-resulthr.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-datadir.o -MD -MP -MF .deps/uniqscanl-datadir.Tpo -c -o uniqscanl-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/uniqscanl-datadir.Tpo .deps/uniqscanl-datadir.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt.o -MD -MP -MF .deps/uniqscanl-getopt.Tpo -c -o uniqscanl-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/uniqscanl-getopt.Tpo .deps/uniqscanl-getopt.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-getopt1.o -MD -MP -MF .deps/uniqscanl-getopt1.Tpo -c -o uniqscanl-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/uniqscanl-getopt1.Tpo .deps/uniqscanl-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -MT uniqscanl-uniqscan.o -MD -MP -MF .deps/uniqscanl-uniqscan.Tpo -c -o uniqscanl-uniqscan.o `test -f 'uniqscan.c' || echo './'`uniqscan.c mv -f .deps/uniqscanl-uniqscan.Tpo .deps/uniqscanl-uniqscan.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lz -lbz2 -lm libtool: link: gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DMAX_READLENGTH=250 -DGSNAP=1 -DLARGE_GENOMES=1 -O3 -o uniqscanl uniqscanl-except.o uniqscanl-assert.o uniqscanl-mem.o uniqscanl-intlist.o uniqscanl-list.o uniqscanl-littleendian.o uniqscanl-bigendian.o uniqscanl-univinterval.o uniqscanl-interval.o uniqscanl-uintlist.o uniqscanl-uint8list.o uniqscanl-stopwatch.o uniqscanl-access.o uniqscanl-iit-read-univ.o uniqscanl-iit-read.o uniqscanl-md5.o uniqscanl-bzip2.o uniqscanl-sequence.o uniqscanl-reader.o uniqscanl-genomicpos.o uniqscanl-compress.o uniqscanl-genome.o uniqscanl-genome_hr.o uniqscanl-genome_sites.o uniqscanl-bitpack64-read.o uniqscanl-indexdb.o uniqscanl-indexdb_hr.o uniqscanl-oligo.o uniqscanl-chrom.o uniqscanl-segmentpos.o uniqscanl-chrnum.o uniqscanl-maxent_hr.o uniqscanl-mapq.o uniqscanl-shortread.o uniqscanl-substring.o uniqscanl-stage3hr.o uniqscanl-spanningelt.o uniqscanl-cmet.o uniqscanl-atoi.o uniqscanl-maxent.o uniqscanl-pair.o uniqscanl-pairpool.o uniqscanl-diag.o uniqscanl-diagpool.o uniqscanl-orderstat.o uniqscanl-oligoindex_hr.o uniqscanl-cellpool.o uniqscanl-stage2.o uniqscanl-intron.o uniqscanl-boyer-moore.o uniqscanl-changepoint.o uniqscanl-pbinom.o uniqscanl-dynprog.o uniqscanl-translation.o uniqscanl-doublelist.o uniqscanl-smooth.o uniqscanl-chimera.o uniqscanl-stage3.o uniqscanl-splicestringpool.o uniqscanl-splicetrie_build.o uniqscanl-splicetrie.o uniqscanl-splice.o uniqscanl-indel.o uniqscanl-bitpack64-access.o uniqscanl-sarray-read.o uniqscanl-stage1hr.o uniqscanl-resulthr.o uniqscanl-datadir.o uniqscanl-getopt.o uniqscanl-getopt1.o uniqscanl-uniqscan.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-except.o -MD -MP -MF .deps/snpindex-except.Tpo -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/snpindex-except.Tpo .deps/snpindex-except.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-assert.o -MD -MP -MF .deps/snpindex-assert.Tpo -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/snpindex-assert.Tpo .deps/snpindex-assert.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-mem.o -MD -MP -MF .deps/snpindex-mem.Tpo -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/snpindex-mem.Tpo .deps/snpindex-mem.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-intlist.o -MD -MP -MF .deps/snpindex-intlist.Tpo -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c mv -f .deps/snpindex-intlist.Tpo .deps/snpindex-intlist.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-list.o -MD -MP -MF .deps/snpindex-list.Tpo -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/snpindex-list.Tpo .deps/snpindex-list.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-littleendian.o -MD -MP -MF .deps/snpindex-littleendian.Tpo -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/snpindex-littleendian.Tpo .deps/snpindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bigendian.o -MD -MP -MF .deps/snpindex-bigendian.Tpo -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/snpindex-bigendian.Tpo .deps/snpindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-univinterval.o -MD -MP -MF .deps/snpindex-univinterval.Tpo -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/snpindex-univinterval.Tpo .deps/snpindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-interval.o -MD -MP -MF .deps/snpindex-interval.Tpo -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/snpindex-interval.Tpo .deps/snpindex-interval.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-uintlist.o -MD -MP -MF .deps/snpindex-uintlist.Tpo -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c mv -f .deps/snpindex-uintlist.Tpo .deps/snpindex-uintlist.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-stopwatch.o -MD -MP -MF .deps/snpindex-stopwatch.Tpo -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/snpindex-stopwatch.Tpo .deps/snpindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-access.o -MD -MP -MF .deps/snpindex-access.Tpo -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/snpindex-access.Tpo .deps/snpindex-access.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read-univ.o -MD -MP -MF .deps/snpindex-iit-read-univ.Tpo -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/snpindex-iit-read-univ.Tpo .deps/snpindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-iit-read.o -MD -MP -MF .deps/snpindex-iit-read.Tpo -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/snpindex-iit-read.Tpo .deps/snpindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genomicpos.o -MD -MP -MF .deps/snpindex-genomicpos.Tpo -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/snpindex-genomicpos.Tpo .deps/snpindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress.o -MD -MP -MF .deps/snpindex-compress.Tpo -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/snpindex-compress.Tpo .deps/snpindex-compress.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-compress-write.o -MD -MP -MF .deps/snpindex-compress-write.Tpo -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c mv -f .deps/snpindex-compress-write.Tpo .deps/snpindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome_hr.o -MD -MP -MF .deps/snpindex-genome_hr.Tpo -c -o snpindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/snpindex-genome_hr.Tpo .deps/snpindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-read.o -MD -MP -MF .deps/snpindex-bitpack64-read.Tpo -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/snpindex-bitpack64-read.Tpo .deps/snpindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bitpack64-write.o -MD -MP -MF .deps/snpindex-bitpack64-write.Tpo -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c: In function ‘Bitpack64_write_vert’: bitpack64-write.c:4146:38: warning: passing argument 2 of ‘reorder_values_vertically’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4146 | reorder_values_vertically(vertical,horizontal); | ^~~~~~~~~~ bitpack64-write.c:4091:70: note: expected ‘Positionsptr_T *’ {aka ‘unsigned int *’} but argument is of type ‘const UINT4 *’ {aka ‘const unsigned int *’} 4091 | reorder_values_vertically (Positionsptr_T *vertical, Positionsptr_T *horizontal) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~ mv -f .deps/snpindex-bitpack64-write.Tpo .deps/snpindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb.o -MD -MP -MF .deps/snpindex-indexdb.Tpo -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/snpindex-indexdb.Tpo .deps/snpindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-indexdb-write.o -MD -MP -MF .deps/snpindex-indexdb-write.Tpo -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c mv -f .deps/snpindex-indexdb-write.Tpo .deps/snpindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-chrom.o -MD -MP -MF .deps/snpindex-chrom.Tpo -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c chrom.c: In function ‘Chrom_from_string’: chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare] 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^~ chrom.c:116:10: note: did you mean to dereference the pointer? 116 | while (p != '\0' && *p >= '0' && *p <= '9') { | ^ mv -f .deps/snpindex-chrom.Tpo .deps/snpindex-chrom.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-md5.o -MD -MP -MF .deps/snpindex-md5.Tpo -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c In function ‘update’, inlined from ‘finish’ at md5.c:241:3, inlined from ‘MD5_compute’ at md5.c:273:10: md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ md5.c: In function ‘MD5_compute’: md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ mv -f .deps/snpindex-md5.Tpo .deps/snpindex-md5.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-bzip2.o -MD -MP -MF .deps/snpindex-bzip2.Tpo -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c mv -f .deps/snpindex-bzip2.Tpo .deps/snpindex-bzip2.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-sequence.o -MD -MP -MF .deps/snpindex-sequence.Tpo -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c mv -f .deps/snpindex-sequence.Tpo .deps/snpindex-sequence.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-genome.o -MD -MP -MF .deps/snpindex-genome.Tpo -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c mv -f .deps/snpindex-genome.Tpo .deps/snpindex-genome.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-datadir.o -MD -MP -MF .deps/snpindex-datadir.Tpo -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/snpindex-datadir.Tpo .deps/snpindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt.o -MD -MP -MF .deps/snpindex-getopt.Tpo -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/snpindex-getopt.Tpo .deps/snpindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-getopt1.o -MD -MP -MF .deps/snpindex-getopt1.Tpo -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/snpindex-getopt1.Tpo .deps/snpindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT snpindex-snpindex.o -MD -MP -MF .deps/snpindex-snpindex.Tpo -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c mv -f .deps/snpindex-snpindex.Tpo .deps/snpindex-snpindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm libtool: link: gcc -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-access.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-genome_hr.o snpindex-bitpack64-read.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-except.o -MD -MP -MF .deps/cmetindex-except.Tpo -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/cmetindex-except.Tpo .deps/cmetindex-except.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-assert.o -MD -MP -MF .deps/cmetindex-assert.Tpo -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/cmetindex-assert.Tpo .deps/cmetindex-assert.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-mem.o -MD -MP -MF .deps/cmetindex-mem.Tpo -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/cmetindex-mem.Tpo .deps/cmetindex-mem.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-littleendian.o -MD -MP -MF .deps/cmetindex-littleendian.Tpo -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/cmetindex-littleendian.Tpo .deps/cmetindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bigendian.o -MD -MP -MF .deps/cmetindex-bigendian.Tpo -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/cmetindex-bigendian.Tpo .deps/cmetindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genomicpos.o -MD -MP -MF .deps/cmetindex-genomicpos.Tpo -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/cmetindex-genomicpos.Tpo .deps/cmetindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-stopwatch.o -MD -MP -MF .deps/cmetindex-stopwatch.Tpo -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/cmetindex-stopwatch.Tpo .deps/cmetindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-access.o -MD -MP -MF .deps/cmetindex-access.Tpo -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/cmetindex-access.Tpo .deps/cmetindex-access.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-univinterval.o -MD -MP -MF .deps/cmetindex-univinterval.Tpo -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/cmetindex-univinterval.Tpo .deps/cmetindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-interval.o -MD -MP -MF .deps/cmetindex-interval.Tpo -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/cmetindex-interval.Tpo .deps/cmetindex-interval.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read-univ.o -MD -MP -MF .deps/cmetindex-iit-read-univ.Tpo -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/cmetindex-iit-read-univ.Tpo .deps/cmetindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-iit-read.o -MD -MP -MF .deps/cmetindex-iit-read.Tpo -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/cmetindex-iit-read.Tpo .deps/cmetindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress.o -MD -MP -MF .deps/cmetindex-compress.Tpo -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/cmetindex-compress.Tpo .deps/cmetindex-compress.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-compress-write.o -MD -MP -MF .deps/cmetindex-compress-write.Tpo -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c mv -f .deps/cmetindex-compress-write.Tpo .deps/cmetindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-genome_hr.o -MD -MP -MF .deps/cmetindex-genome_hr.Tpo -c -o cmetindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/cmetindex-genome_hr.Tpo .deps/cmetindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-read.o -MD -MP -MF .deps/cmetindex-bitpack64-read.Tpo -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/cmetindex-bitpack64-read.Tpo .deps/cmetindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-bitpack64-write.o -MD -MP -MF .deps/cmetindex-bitpack64-write.Tpo -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c: In function ‘Bitpack64_write_vert’: bitpack64-write.c:4146:38: warning: passing argument 2 of ‘reorder_values_vertically’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4146 | reorder_values_vertically(vertical,horizontal); | ^~~~~~~~~~ bitpack64-write.c:4091:70: note: expected ‘Positionsptr_T *’ {aka ‘unsigned int *’} but argument is of type ‘const UINT4 *’ {aka ‘const unsigned int *’} 4091 | reorder_values_vertically (Positionsptr_T *vertical, Positionsptr_T *horizontal) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~ mv -f .deps/cmetindex-bitpack64-write.Tpo .deps/cmetindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb.o -MD -MP -MF .deps/cmetindex-indexdb.Tpo -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/cmetindex-indexdb.Tpo .deps/cmetindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-indexdb-write.o -MD -MP -MF .deps/cmetindex-indexdb-write.Tpo -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c mv -f .deps/cmetindex-indexdb-write.Tpo .deps/cmetindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmet.o -MD -MP -MF .deps/cmetindex-cmet.Tpo -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c mv -f .deps/cmetindex-cmet.Tpo .deps/cmetindex-cmet.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-list.o -MD -MP -MF .deps/cmetindex-list.Tpo -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/cmetindex-list.Tpo .deps/cmetindex-list.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-datadir.o -MD -MP -MF .deps/cmetindex-datadir.Tpo -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/cmetindex-datadir.Tpo .deps/cmetindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt.o -MD -MP -MF .deps/cmetindex-getopt.Tpo -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/cmetindex-getopt.Tpo .deps/cmetindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-getopt1.o -MD -MP -MF .deps/cmetindex-getopt1.Tpo -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/cmetindex-getopt1.Tpo .deps/cmetindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT cmetindex-cmetindex.o -MD -MP -MF .deps/cmetindex-cmetindex.Tpo -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c mv -f .deps/cmetindex-cmetindex.Tpo .deps/cmetindex-cmetindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm libtool: link: gcc -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-genome_hr.o cmetindex-bitpack64-read.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-list.o cmetindex-datadir.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lm gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-except.o -MD -MP -MF .deps/atoiindex-except.Tpo -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c mv -f .deps/atoiindex-except.Tpo .deps/atoiindex-except.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-assert.o -MD -MP -MF .deps/atoiindex-assert.Tpo -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c mv -f .deps/atoiindex-assert.Tpo .deps/atoiindex-assert.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-mem.o -MD -MP -MF .deps/atoiindex-mem.Tpo -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c mv -f .deps/atoiindex-mem.Tpo .deps/atoiindex-mem.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-littleendian.o -MD -MP -MF .deps/atoiindex-littleendian.Tpo -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c mv -f .deps/atoiindex-littleendian.Tpo .deps/atoiindex-littleendian.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bigendian.o -MD -MP -MF .deps/atoiindex-bigendian.Tpo -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c mv -f .deps/atoiindex-bigendian.Tpo .deps/atoiindex-bigendian.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genomicpos.o -MD -MP -MF .deps/atoiindex-genomicpos.Tpo -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c mv -f .deps/atoiindex-genomicpos.Tpo .deps/atoiindex-genomicpos.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-stopwatch.o -MD -MP -MF .deps/atoiindex-stopwatch.Tpo -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c mv -f .deps/atoiindex-stopwatch.Tpo .deps/atoiindex-stopwatch.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-access.o -MD -MP -MF .deps/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘Access_file_exists_p’: access.c:61:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 61 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat mv -f .deps/atoiindex-access.Tpo .deps/atoiindex-access.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-univinterval.o -MD -MP -MF .deps/atoiindex-univinterval.Tpo -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c mv -f .deps/atoiindex-univinterval.Tpo .deps/atoiindex-univinterval.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-interval.o -MD -MP -MF .deps/atoiindex-interval.Tpo -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c mv -f .deps/atoiindex-interval.Tpo .deps/atoiindex-interval.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read-univ.o -MD -MP -MF .deps/atoiindex-iit-read-univ.Tpo -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c mv -f .deps/atoiindex-iit-read-univ.Tpo .deps/atoiindex-iit-read-univ.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-iit-read.o -MD -MP -MF .deps/atoiindex-iit-read.Tpo -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c mv -f .deps/atoiindex-iit-read.Tpo .deps/atoiindex-iit-read.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress.o -MD -MP -MF .deps/atoiindex-compress.Tpo -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c mv -f .deps/atoiindex-compress.Tpo .deps/atoiindex-compress.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-compress-write.o -MD -MP -MF .deps/atoiindex-compress-write.Tpo -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c mv -f .deps/atoiindex-compress-write.Tpo .deps/atoiindex-compress-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-genome_hr.o -MD -MP -MF .deps/atoiindex-genome_hr.Tpo -c -o atoiindex-genome_hr.o `test -f 'genome_hr.c' || echo './'`genome_hr.c mv -f .deps/atoiindex-genome_hr.Tpo .deps/atoiindex-genome_hr.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-read.o -MD -MP -MF .deps/atoiindex-bitpack64-read.Tpo -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c mv -f .deps/atoiindex-bitpack64-read.Tpo .deps/atoiindex-bitpack64-read.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-bitpack64-write.o -MD -MP -MF .deps/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c bitpack64-write.c: In function ‘Bitpack64_write_vert’: bitpack64-write.c:4146:38: warning: passing argument 2 of ‘reorder_values_vertically’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 4146 | reorder_values_vertically(vertical,horizontal); | ^~~~~~~~~~ bitpack64-write.c:4091:70: note: expected ‘Positionsptr_T *’ {aka ‘unsigned int *’} but argument is of type ‘const UINT4 *’ {aka ‘const unsigned int *’} 4091 | reorder_values_vertically (Positionsptr_T *vertical, Positionsptr_T *horizontal) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~ mv -f .deps/atoiindex-bitpack64-write.Tpo .deps/atoiindex-bitpack64-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb.o -MD -MP -MF .deps/atoiindex-indexdb.Tpo -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c mv -f .deps/atoiindex-indexdb.Tpo .deps/atoiindex-indexdb.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-indexdb-write.o -MD -MP -MF .deps/atoiindex-indexdb-write.Tpo -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c mv -f .deps/atoiindex-indexdb-write.Tpo .deps/atoiindex-indexdb-write.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoi.o -MD -MP -MF .deps/atoiindex-atoi.Tpo -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c mv -f .deps/atoiindex-atoi.Tpo .deps/atoiindex-atoi.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-list.o -MD -MP -MF .deps/atoiindex-list.Tpo -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/atoiindex-list.Tpo .deps/atoiindex-list.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-datadir.o -MD -MP -MF .deps/atoiindex-datadir.Tpo -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c mv -f .deps/atoiindex-datadir.Tpo .deps/atoiindex-datadir.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt.o -MD -MP -MF .deps/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c mv -f .deps/atoiindex-getopt.Tpo .deps/atoiindex-getopt.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-getopt1.o -MD -MP -MF .deps/atoiindex-getopt1.Tpo -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c mv -f .deps/atoiindex-getopt1.Tpo .deps/atoiindex-getopt1.Po gcc -DHAVE_CONFIG_H -I. -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -MT atoiindex-atoiindex.o -MD -MP -MF .deps/atoiindex-atoiindex.Tpo -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c mv -f .deps/atoiindex-atoiindex.Tpo .deps/atoiindex-atoiindex.Po /bin/sh ../libtool --tag=CC --mode=link gcc -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm libtool: link: gcc -DGMAPDB=\"/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/share\" -DUTILITYP=1 -O3 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-genome_hr.o atoiindex-bitpack64-read.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-list.o atoiindex-datadir.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lm make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/src' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin' libtool: install: /usr/bin/install -c gmap /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/gmap libtool: install: /usr/bin/install -c gmapl /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/gmapl libtool: install: /usr/bin/install -c get-genome /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/get-genome libtool: install: /usr/bin/install -c gmapindex /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/gmapindex libtool: install: /usr/bin/install -c iit_store /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/iit_store libtool: install: /usr/bin/install -c iit_get /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/iit_get libtool: install: /usr/bin/install -c iit_dump /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/iit_dump libtool: install: /usr/bin/install -c gsnap /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/gsnap libtool: install: /usr/bin/install -c gsnapl /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/gsnapl libtool: install: /usr/bin/install -c uniqscan /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/uniqscan libtool: install: /usr/bin/install -c uniqscanl /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/uniqscanl libtool: install: /usr/bin/install -c snpindex /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/snpindex libtool: install: /usr/bin/install -c cmetindex /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/cmetindex libtool: install: /usr/bin/install -c atoiindex /home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin/atoiindex make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/src' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/src' Making install in util make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/util' cp gmap_compress.pl gmap_compress chmod +x gmap_compress cp gmap_uncompress.pl gmap_uncompress chmod +x gmap_uncompress cp gmap_process.pl gmap_process chmod +x gmap_process cp gmap_setup.pl gmap_setup chmod +x gmap_setup cp gmap_build.pl gmap_build chmod +x gmap_build cp gmap_reassemble.pl gmap_reassemble chmod +x gmap_reassemble cp md_coords.pl md_coords chmod +x md_coords cp fa_coords.pl fa_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites cp psl_introns.pl psl_introns chmod +x psl_introns cp psl_genes.pl psl_genes chmod +x psl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/util' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin' /usr/bin/install -c gmap_compress gmap_uncompress gmap_process gmap_setup gmap_build gmap_reassemble md_coords fa_coords psl_splicesites psl_introns psl_genes gtf_splicesites gtf_introns gtf_genes gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/../inst/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/util' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/util' Making install in tests make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/tests' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/tests' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap/tests' make[2]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap' make[3]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap' make[2]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap' make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/gmapR/src/gmap' installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-gmapR/00new/gmapR/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘directory’ in package ‘gmapR’ Creating a generic function for ‘bamPaths’ from package ‘Rsamtools’ in package ‘gmapR’ Note: ... may be used in an incorrect context ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gmapR)