* 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... 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(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 ‘Littleendian_write_char’: littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint’: littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8’: littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 44 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 57 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:63:3: warning: ignoring return value of ‘write’, 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 ‘Bigendian_write_char’: bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint’: bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 176 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 260 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 328 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:445:3: warning: ignoring return value of ‘read’, 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 ‘Access_file_exists_p’: access.c:71:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration] 71 | if (stat64(filename,&sb) == 0) { | ^~~~~~ | stat access.c: In function ‘copy_memory_from_file’: access.c:530:7: warning: ignoring return value of ‘fread’, 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 ‘fread’, 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 ‘fread’, 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 ‘fread’, 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 ‘fread’, 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 ‘fread’, 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 ‘read_tree_univ’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT’ 1035 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 1037 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 1038 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 1039 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 1040 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT8’ 1088 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:25:27: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT8’ 1089 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 1090 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:21:26: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT’ 1099 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:21:26: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT’ 1101 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 1103 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT’ 1163 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read_words_debug’: littleendian.h:21:26: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT’ 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 ‘IIT_read_divint’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 2312 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 2570 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1623:2: warning: ignoring return value of ‘fread’, 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 ‘fread’, 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 ‘fread’, 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 ‘fread’, 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 ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1627 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1708:7: warning: ignoring return value of ‘fread’, 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 ‘fread’, 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 ‘fread’, 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 ‘fread’, 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 ‘read_words’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT8’ 1820 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:21:26: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT’ 1826 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2207:5: warning: ignoring return value of ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘read’, 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 ‘IIT_debug’: littleendian.h:20:25: warning: ignoring return value of ‘fread’, 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 ‘FREAD_INT’ 2981 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:25:27: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT8’ 1964 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:21:26: warning: ignoring return value of ‘fread’, 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 ‘FREAD_UINT’ 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 ‘fill_buffer’: genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10582 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 458 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple’: genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10713 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 10833 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 11002 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11301:7: warning: ignoring return value of ‘read’, 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 ‘positions_read_multiple’: indexdb.c:1751:5: warning: ignoring return value of ‘read’, 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 ‘positions_move_absolute’: indexdb_hr.c:593:55: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘Positionsptr_T’ {aka ‘unsigned int’} [-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 ‘positions_read_multiple’: indexdb_hr.c:624:5: warning: ignoring return value of ‘read’, 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 ‘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') { | ^ 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 ‘SAM_header_change_HD_tosorted’: samheader.c:201:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 201 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:206:5: warning: ignoring return value of ‘fread’, 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'