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Gentoo's Bugzilla – Attachment 612438 Details for
Bug 708626
sci-biology/gmap-2015.12.31.5 : fails to build with -fno-common or gcc-10
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sci-biology:gmap-2015.12.31.5:20200207-005303.log
sci-biology:gmap-2015.12.31.5:20200207-005303.log (text/plain), 64.42 KB, created by
Toralf Förster
on 2020-02-07 18:19:58 UTC
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hide
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Description:
sci-biology:gmap-2015.12.31.5:20200207-005303.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2020-02-07 18:19:58 UTC
Size:
64.42 KB
patch
obsolete
> * Package: sci-biology/gmap-2015.12.31.5 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking gmap-gsnap-2015-12-31.v5.tar.gz to /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work >>>> Source unpacked in /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work >>>> Preparing source in /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31 ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31 ... > * econf: updating gmap-2015-12-31/config/config.guess with /usr/share/gnuconfig/config.guess > * econf: updating gmap-2015-12-31/config/config.sub with /usr/share/gnuconfig/config.sub >./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --docdir=/usr/share/doc/gmap-2015.12.31.5 --htmldir=/usr/share/doc/gmap-2015.12.31.5/html --libdir=/usr/lib64 >checking package version... 2015-12-31 >loading default site script ./config.site >checking CFLAGS... -O2 -pipe -march=native -fno-common >checking MPI_CFLAGS... >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking target system type... x86_64-pc-linux-gnu >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking for C compiler default output file name... a.out >checking whether the C compiler works... yes >checking whether we are cross compiling... no >checking for suffix of executables... >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking for special C compiler options needed for large files... no >checking for _FILE_OFFSET_BITS value needed for large files... no >checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c >checking whether build environment is sane... yes >checking for a thread-safe mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking for style of include used by make... GNU >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking bindir... /usr/bin >checking for a working version of perl... /usr/bin/perl >checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc >checking whether we are using the GNU C compiler... (cached) yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed >checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes >checking for mpicc... no >checking for hcc... no >checking for mpxlc_r... no >checking for mpxlc... no >checking for mpcc... no >checking for cmpicc... no >checking for cc... /usr/bin/cc >checking for MPI_Init... no >checking for MPI_Init in -lmpi... no >checking for MPI_Init in -lmpich... no >checking for a sed that does not truncate output... /bin/sed >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/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 for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking how to run the C preprocessor... x86_64-pc-linux-gnu-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 x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether stripping libraries is possible... yes >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... yes >checking for rint in -lm... yes >checking whether to use MPI_File for input... not specified so enabled by default >checking for pthreads feature... not specified so enabled by default >checking for the pthreads library -lpthreads... no >checking whether pthreads work without any flags... no >checking whether pthreads work with -Kthread... no >checking whether pthreads work with -kthread... no >checking for the pthreads library -llthread... no >checking whether pthreads work with -pthread... yes >checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE >checking if more special flags are required for pthreads... no >checking for cc_r... x86_64-pc-linux-gnu-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 alloca is enabled... not specified so enabled by default >checking for working alloca.h... yes >checking for alloca... yes >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 SHM_NORESERVE in shmget... yes >checking for ceil... yes >checking for floor... yes >checking for index... yes >checking for log... yes >checking for madvise... yes >checking for memcpy... yes >checking for memmove... yes >checking for memset... yes >checking for munmap... yes >checking for pow... yes >checking for rint... yes >checking for stat64... yes >checking for strtoul... yes >checking for sysconf... yes >checking for sysctl... yes >checking for sigaction... yes >checking for shmget... yes >checking for shmctl... yes >checking for shmat... yes >checking for shmdt... yes >checking for semget... yes >checking for semctl... yes >checking for semop... 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 >checking whether -mpopcnt compiler flag works... 6B8B4567 clz=1 ctz=0 popcount=17 yes >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 compiler is defective and requires an immediate in sse2 shift commands... no >checking whether ssse3 is enabled... not specified so enabled by default >checking whether sse4.1 is enabled... not specified so enabled by default >checking whether sse4.2 is enabled... not specified so enabled by default >checking whether avx is enabled... not specified so enabled by default >checking whether avx2 is enabled... not specified so enabled by default >checking whether simd is enabled... not specified so enabled by default >checking for x86 cpuid 0x00000001 output... 306f2:5100800:7ffefbff:bfebfbff >checking whether mmx is enabled and supported by CPU... yes >checking whether sse is enabled and supported by CPU... yes >checking whether sse2 is enabled and supported by CPU... yes >checking whether sse3 is enabled and supported by CPU... yes >checking whether ssse3 is enabled and supported by CPU... yes >checking whether sse4.1 is enabled and supported by CPU... yes >checking whether sse4.2 is enabled and supported by CPU... yes >checking whether avx is enabled and supported by CPU... yes >checking for x86-AVX xgetbv 0x00000000 output... 7:0 >checking whether avx is supported by operating system... yes >checking whether popcnt is enabled and supported by CPU... yes >checking for x86 cpuid 0x80000001 output... 0:0:21:2c100800 >checking whether lzcnt is enabled and supported by CPU... yes >checking for x86 cpuid 0x00000007 output... 0:0:0:0 >checking whether avx2 is enabled and supported by CPU... no >checking whether bmi1 is enabled and supported by CPU... no >checking whether bmi2 is enabled and supported by CPU... no >checking whether C compiler accepts -mmmx... yes >checking for mmintrin.h header file... yes >checking whether C compiler accepts -msse... yes >checking for xmmintrin.h header file... yes >checking whether C compiler accepts -msse2... yes >checking for emmintrin.h header file... yes >checking whether C compiler accepts -msse3... yes >checking for pmmintrin.h header file... yes >checking whether C compiler accepts -mssse3... yes >checking for tmmintrin.h header file... yes >checking whether C compiler accepts -msse4.1... yes >checking for smmintrin.h header file... yes >checking whether C compiler accepts -msse4.2... yes >checking for nmmintrin.h header file... yes >checking whether C compiler accepts -mavx... yes >checking for immintrin.h header file... yes >checking gmapdb... /usr/share >checking MAX_READLENGTH... 300 >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 >configure: creating ./config.status >config.status: creating Makefile >config.status: creating src/Makefile >config.status: creating mpi/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_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/ensembl_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 >checking Standard compiler and flags to be used... x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common >checking Standard linker flags to be used... >checking MPI compiler and flags to be used... /usr/bin/cc >checking MPI linker flags to be used... >checking pthread compiler flags to be used... -pthread >checking popcnt compiler flags to be used... -mpopcnt >checking SIMD features available on computer... mmx sse sse2 sse3 ssse3 sse4.1 sse4.2 avx >checking SIMD compiler flags to be used... -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31 ... >make -j1 >Making all in src >make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31/src' >make all-am >make[2]: Entering directory '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31/src' >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c >littleendian.c: In function âLittleendian_write_charâ: >littleendian.c:14:3: warning: ignoring return value of âwriteâ, declared with attribute warn_unused_result [-Wunused-result] > 14 | write(fd,buf,1); > | ^~~~~~~~~~~~~~~ >littleendian.c: In function âLittleendian_write_uintâ: >littleendian.c:27:3: warning: ignoring return value of âwriteâ, declared with attribute warn_unused_result [-Wunused-result] > 27 | write(fd,buf,4); > | ^~~~~~~~~~~~~~~ >littleendian.c: In function âLittleendian_write_uint8â: >littleendian.c:44:3: warning: ignoring return value of âwriteâ, declared with attribute warn_unused_result [-Wunused-result] > 44 | write(fd,buf,8); > | ^~~~~~~~~~~~~~~ >littleendian.c: In function âLittleendian_write_uint8_as_uintâ: >littleendian.c:57:3: warning: ignoring return value of âwriteâ, declared with attribute warn_unused_result [-Wunused-result] > 57 | write(fd,buf,4); > | ^~~~~~~~~~~~~~~ >littleendian.c:63:3: warning: ignoring return value of âwriteâ, declared with attribute warn_unused_result [-Wunused-result] > 63 | write(fd,buf,4); > | ^~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c >bigendian.c: In function âBigendian_write_charâ: >bigendian.c:16:3: warning: ignoring return value of âwriteâ, declared with attribute warn_unused_result [-Wunused-result] > 16 | write(fd,buf,1); > | ^~~~~~~~~~~~~~~ >bigendian.c: In function âBigendian_write_uintâ: >bigendian.c:176:3: warning: ignoring return value of âwriteâ, declared with attribute warn_unused_result [-Wunused-result] > 176 | write(fd,buf,4); > | ^~~~~~~~~~~~~~~ >bigendian.c: In function âBigendian_fileio_read_uintâ: >bigendian.c:260:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 260 | read(fd,buf,4); > | ^~~~~~~~~~~~~~ >bigendian.c: In function âBigendian_write_uint8â: >bigendian.c:328:3: warning: ignoring return value of âwriteâ, declared with attribute warn_unused_result [-Wunused-result] > 328 | write(fd,buf,8); > | ^~~~~~~~~~~~~~~ >bigendian.c: In function âBigendian_fileio_read_uint8â: >bigendian.c:445:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 445 | read(fd,buf,8); > | ^~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c >access.c: In function âAccess_file_exists_pâ: >access.c:71:7: warning: implicit declaration of function âstat64â; did you mean âstatâ? [-Wimplicit-function-declaration] > 71 | if (stat64(filename,&sb) == 0) { > | ^~~~~~ > | stat >access.c: In function âcopy_memory_from_fileâ: >access.c:530:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 530 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >access.c:535:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 535 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >access.c:541:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 541 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >access.c:546:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 546 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >access.c:552:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 552 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >access.c:557:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 557 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-filestring.o `test -f 'filestring.c' || echo './'`filestring.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c >In file included from iit-read-univ.c:11: >iit-read-univ.c: In function âread_tree_univâ: >littleendian.h:21:26: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1035:2: note: in expansion of macro âFREAD_UINTâ > 1035 | FREAD_UINT(&uint4,fp); > | ^~~~~~~~~~ >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1037:2: note: in expansion of macro âFREAD_INTâ > 1037 | FREAD_INT(&(new->nodes[i].a),fp); > | ^~~~~~~~~ >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1038:2: note: in expansion of macro âFREAD_INTâ > 1038 | FREAD_INT(&(new->nodes[i].b),fp); > | ^~~~~~~~~ >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1039:2: note: in expansion of macro âFREAD_INTâ > 1039 | FREAD_INT(&(new->nodes[i].leftindex),fp); > | ^~~~~~~~~ >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1040:2: note: in expansion of macro âFREAD_INTâ > 1040 | FREAD_INT(&(new->nodes[i].rightindex),fp); > | ^~~~~~~~~ >iit-read-univ.c: In function âread_intervals_univâ: >littleendian.h:25:27: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 25 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1088:7: note: in expansion of macro âFREAD_UINT8â > 1088 | FREAD_UINT8(&(new->intervals[i].low),fp); > | ^~~~~~~~~~~ >littleendian.h:25:27: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 25 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1089:7: note: in expansion of macro âFREAD_UINT8â > 1089 | FREAD_UINT8(&(new->intervals[i].high),fp); > | ^~~~~~~~~~~ >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1090:7: note: in expansion of macro âFREAD_INTâ > 1090 | FREAD_INT(&(new->intervals[i].type),fp); > | ^~~~~~~~~ >littleendian.h:21:26: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1099:7: note: in expansion of macro âFREAD_UINTâ > 1099 | FREAD_UINT(&uint4,fp); > | ^~~~~~~~~~ >littleendian.h:21:26: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1101:7: note: in expansion of macro âFREAD_UINTâ > 1101 | FREAD_UINT(&uint4,fp); > | ^~~~~~~~~~ >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1103:7: note: in expansion of macro âFREAD_INTâ > 1103 | FREAD_INT(&(new->intervals[i].type),fp); > | ^~~~~~~~~ >iit-read-univ.c: In function âread_wordsâ: >littleendian.h:21:26: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1163:3: note: in expansion of macro âFREAD_UINTâ > 1163 | FREAD_UINT(&length,fp); > | ^~~~~~~~~~ >iit-read-univ.c: In function âread_annotationsâ: >iit-read-univ.c:1385:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1385 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1389:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1389 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1393:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1393 | read(new->fd,new->labels,new->label_length*sizeof(char)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1397:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1397 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1401:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1401 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >In file included from iit-read-univ.c:11: >iit-read-univ.c: In function âread_words_debugâ: >littleendian.h:21:26: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read-univ.c:1245:3: note: in expansion of macro âFREAD_UINTâ > 1245 | FREAD_UINT(&length,fp); > | ^~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c >In file included from iit-read.c:12: >iit-read.c: In function âIIT_read_divintâ: >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2312:5: note: in expansion of macro âFREAD_INTâ > 2312 | FREAD_INT(&version,fp); > | ^~~~~~~~~ >iit-read.c: In function âIIT_readâ: >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2570:5: note: in expansion of macro âFREAD_INTâ > 2570 | FREAD_INT(&new->version,fp); > | ^~~~~~~~~ >iit-read.c: In function âread_treeâ: >iit-read.c:1623:2: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1623 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1624:2: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1624 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1625:2: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1625 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1626:2: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1626 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1627:2: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1627 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c: In function âread_intervalsâ: >iit-read.c:1708:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1708 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1709:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1709 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1711:2: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1711 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1715:7: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1715 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >In file included from iit-read.c:12: >iit-read.c: In function âread_wordsâ: >littleendian.h:25:27: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 25 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1820:5: note: in expansion of macro âFREAD_UINT8â > 1820 | FREAD_UINT8(&length8,fp); > | ^~~~~~~~~~~ >littleendian.h:21:26: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1826:5: note: in expansion of macro âFREAD_UINTâ > 1826 | FREAD_UINT(&length,fp); > | ^~~~~~~~~~ >iit-read.c: In function âread_annotationsâ: >iit-read.c:2207:5: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2207 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2211:5: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2211 | read(new->fd,new->values,new->value_length*sizeof(char)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2216:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2216 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2222:5: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2222 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2227:5: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2227 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2238:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2238 | read(new->fd,new->labels,new->label_length*sizeof(char)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2244:5: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2244 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2249:5: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2249 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2260:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 2260 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >In file included from iit-read.c:12: >iit-read.c: In function âIIT_debugâ: >littleendian.h:20:25: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:2981:5: note: in expansion of macro âFREAD_INTâ > 2981 | FREAD_INT(&new->version,fp); > | ^~~~~~~~~ >iit-read.c: In function âread_words_debugâ: >littleendian.h:25:27: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 25 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1964:5: note: in expansion of macro âFREAD_UINT8â > 1964 | FREAD_UINT8(&length8,fp); > | ^~~~~~~~~~~ >littleendian.h:21:26: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >iit-read.c:1969:5: note: in expansion of macro âFREAD_UINTâ > 1969 | FREAD_UINT(&length,fp); > | ^~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c >genome.c: In function âfill_bufferâ: >genome.c:10582:7: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] >10582 | read(this->fd,gbuffer1,length); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >genome.c: In function âgenomecomp_read_currentâ: >genome.c:458:3: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 458 | read(this->fd,buffer,4); > | ^~~~~~~~~~~~~~~~~~~~~~~ >genome.c: In function âGenome_fill_buffer_simpleâ: >genome.c:10713:7: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] >10713 | read(this->fd,gbuffer1,length); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >genome.c: In function âGenome_fill_buffer_simple_altâ: >genome.c:10833:7: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] >10833 | read(genomealt->fd,gbuffer1,length); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >genome.c: In function âGenome_get_charâ: >genome.c:11002:7: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] >11002 | read(this->fd,gbuffer1,/*length*/1); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >genome.c: In function âGenome_ntcountsâ: >genome.c:11301:7: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] >11301 | read(this->fd,gbuffer,length); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-popcount.o `test -f 'popcount.c' || echo './'`popcount.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c >indexdb.c: In function âpositions_read_multipleâ: >indexdb.c:1751:5: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 1751 | read(positions_fd,buffer,4); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c >indexdb_hr.c: In function âpositions_move_absoluteâ: >indexdb_hr.c:593:55: warning: format â%zdâ expects argument of type âsigned size_tâ, but argument 3 has type âPositionsptr_Tâ {aka âunsigned intâ} [-Wformat=] > 593 | fprintf(stderr,"Attempted to do lseek on offset %zd*%d=%zd\n", > | ~~^ > | | > | long int > | %d > 594 | ptr,(int) sizeof(Univcoord_T),offset); > | ~~~ > | | > | Positionsptr_T {aka unsigned int} >indexdb_hr.c: In function âpositions_read_multipleâ: >indexdb_hr.c:624:5: warning: ignoring return value of âreadâ, declared with attribute warn_unused_result [-Wunused-result] > 624 | read(positions_fd,buffer,4); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c >chrom.c: In function âChrom_from_stringâ: >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') { > | ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-output.o `test -f 'output.c' || echo './'`output.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c >samheader.c: In function âSAM_header_change_HD_tosortedâ: >samheader.c:201:5: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 201 | fread(buffer,sizeof(char),CHUNK,input); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >samheader.c:206:5: warning: ignoring return value of âfreadâ, declared with attribute warn_unused_result [-Wunused-result] > 206 | fread(buffer,sizeof(char),headerlen,input); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c >/bin/sh ../libtool --tag=CC --mode=link x86_64-pc-linux-gnu-gcc -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -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-filestring.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-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.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-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.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: x86_64-pc-linux-gnu-gcc -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -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-filestring.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-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.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-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lz -lbz2 -lm -pthread >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: gmap-dynprog_end.o:(.bss+0x0): multiple definition of `homopolymerp'; gmap-dynprog_single.o:(.bss+0x0): first defined here >collect2: error: ld returned 1 exit status >make[2]: *** [Makefile:1300: gmap] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31/src' >make[1]: *** [Makefile:1195: all] Error 2 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31/src' >make: *** [Makefile:315: all-recursive] Error 1 > * ERROR: sci-biology/gmap-2015.12.31.5::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/gmap-2015.12.31.5::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/gmap-2015.12.31.5::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:gmap-2015.12.31.5:20200207-005303.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31' > * S: '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31'
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