* Package: sci-biology/gmap-2020.10.27 * 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-2020-10-27.tar.gz to /var/tmp/portage/sci-biology/gmap-2020.10.27/work >>> Source unpacked in /var/tmp/portage/sci-biology/gmap-2020.10.27/work >>> Preparing source in /var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27 ... * Applying gmap-2020.10.27-fno-common.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27 ... * econf: updating gmap-2020-10-27/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating gmap-2020-10-27/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 --disable-silent-rules --docdir=/usr/share/doc/gmap-2020.10.27 --htmldir=/usr/share/doc/gmap-2020.10.27/html --libdir=/usr/lib64 configure: loading site script /usr/share/config.site checking package version... 2020-10-27 loading default site script ./config.site checking CFLAGS... -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security 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 non-Intel CPU... no checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether 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/python3.7/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 whether make supports nested variables... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none checking whether to enable maintainer-specific portions of Makefiles... no 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 C compiler vendor... gnu 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 how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required 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 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 for inline... inline 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 disabled by default 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... no 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 whether C compiler accepts -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -mpopcnt... yes checking for __builtin_popcount... yes checking for __builtin_clz... yes checking for __builtin_ctz... yes checking for bsr instruction in assembly... yes checking compiler is defective and requires an immediate in sse2 shift commands... no checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... not specified so enabled by default checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking gmapdb... /usr/share checking MAX_STACK_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 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.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_transcript_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 checking standard compiler and flags to be used... x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security checking standard linker flags to be used... checking pthread compiler flags to be used... -pthread checking popcnt flags to be used... -mpopcnt checking compile level... avx2 checking AVX2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27 ... make -j1 Making all in src make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/src' make all-am make[2]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/src' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -DMAIN=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c x86_64-pc-linux-gnu-gcc -DMAIN=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o cpuid cpuid-cpuid.o -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo './'`gmap_select.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gmap gmap-cpuid.o gmap-gmap_select.o -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo './'`gmapl_select.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-chrom.o `test -f 'chrom.c' || echo './'`chrom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo './'`get-genome.c x86_64-pc-linux-gnu-gcc -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-getopt.o get_genome-getopt1.o get_genome-get-genome.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c In file included from regiondb-write.c:19: regiondb-write.c: In function ‘Region_read’: littleendian.h:22:31: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:478:3: note: in expansion of macro ‘FREAD_USHORTS’ 478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp); | ^~~~~~~~~~~~~ littleendian.h:22:31: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:479:3: note: in expansion of macro ‘FREAD_USHORTS’ 479 | FREAD_USHORTS(buffer->positions,REGION_LENGTH,fp); | ^~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-table.o `test -f 'table.c' || echo './'`table.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo './'`tableuint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo './'`tableuint8.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo './'`tableint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo './'`gmapindex.c x86_64-pc-linux-gnu-gcc -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-genome128_hr.o gmapindex-genome128_consec.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-regiondb.o gmapindex-regiondb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo './'`indexdb-cat.c x86_64-pc-linux-gnu-gcc -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-getopt.o indexdb_cat-getopt1.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo './'`iit-write-univ.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo './'`iit-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-tableint.o `test -f 'tableint.c' || echo './'`tableint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-table.o `test -f 'table.c' || echo './'`table.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-chrom.o `test -f 'chrom.c' || echo './'`chrom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo './'`iit_store.c x86_64-pc-linux-gnu-gcc -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-getopt.o iit_store-getopt1.o iit_store-iit_store.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo './'`iit_get.c x86_64-pc-linux-gnu-gcc -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-getopt.o iit_get-getopt1.o iit_get-iit_get.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo './'`iit_dump.c x86_64-pc-linux-gnu-gcc -pthread -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-getopt.o iit_dump-getopt1.o iit_dump-iit_dump.o -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo './'`gsnap_select.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo './'`cpuid.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo './'`gsnapl_select.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-chrom.o `test -f 'chrom.c' || echo './'`chrom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo './'`snpindex.c x86_64-pc-linux-gnu-gcc -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-genome128_hr.o snpindex-genome128_consec.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-getopt.o snpindex-getopt1.o snpindex-snpindex.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c In file included from regiondb-write.c:19: regiondb-write.c: In function ‘Region_read’: littleendian.h:22:31: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:478:3: note: in expansion of macro ‘FREAD_USHORTS’ 478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp); | ^~~~~~~~~~~~~ littleendian.h:22:31: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:479:3: note: in expansion of macro ‘FREAD_USHORTS’ 479 | FREAD_USHORTS(buffer->positions,REGION_LENGTH,fp); | ^~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo './'`cmet.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo './'`cmetindex.c x86_64-pc-linux-gnu-gcc -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-genome128_hr.o cmetindex-genome128_consec.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-regiondb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-getopt.o cmetindex-getopt1.o cmetindex-cmetindex.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo './'`bitpack64-incr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo './'`indexdb-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-regiondb-write.o `test -f 'regiondb-write.c' || echo './'`regiondb-write.c In file included from regiondb-write.c:19: regiondb-write.c: In function ‘Region_read’: littleendian.h:22:31: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:478:3: note: in expansion of macro ‘FREAD_USHORTS’ 478 | FREAD_USHORTS(buffer->offsets,offsets_size,fp); | ^~~~~~~~~~~~~ littleendian.h:22:31: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 22 | #define FREAD_USHORTS(a,n,fp) fread(a,sizeof(UINT2),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ regiondb-write.c:479:3: note: in expansion of macro ‘FREAD_USHORTS’ 479 | FREAD_USHORTS(buffer->positions,REGION_LENGTH,fp); | ^~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo './'`atoi.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo './'`atoiindex.c x86_64-pc-linux-gnu-gcc -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-genome128_hr.o atoiindex-genome128_consec.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-regiondb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-getopt.o atoiindex-getopt1.o atoiindex-atoiindex.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo './'`bitpack64-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o trindex-trindex.o `test -f 'trindex.c' || echo './'`trindex.c x86_64-pc-linux-gnu-gcc -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-getopt.o trindex-getopt1.o trindex-trindex.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-samread.o `test -f 'samread.c' || echo './'`samread.c samread.c: In function ‘Samread_flag_duplicate’: samread.c:1186:29: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 1186 | sprintf(newflag_string,"%u",flag | DUPLICATE_READ); | ^ In file included from /usr/include/stdio.h:866, from samread.c:6: /usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 11 bytes into a destination of size 10 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o sam_sort-sam_sort.o `test -f 'sam_sort.c' || echo './'`sam_sort.c sam_sort.c: In function ‘process_no_dedup’: sam_sort.c:1160:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1160 | fgets(line,linelen+1,fp_sam); /* Will read linelen characters with '\n' and then '\0' */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sam_sort.c: In function ‘print_results’: sam_sort.c:1012:8: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1012 | fgets(line,linelen+1,fp_sam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sam_sort.c:1029:8: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1029 | fgets(line,linelen+1,fp_sam); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ sam_sort.c: In function ‘read_sam_files_for_hashseq’: sam_sort.c:1369:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1369 | fgets(line,linelen+1,fp_sam); /* Will read linelen characters with '\n' and then '\0' */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -pthread -DGMAPDB=\"/usr/share\" -DUTILITYP=1 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o sam_sort sam_sort-except.o sam_sort-assert.o sam_sort-mem.o sam_sort-littleendian.o sam_sort-bigendian.o sam_sort-intlist.o sam_sort-list.o sam_sort-stopwatch.o sam_sort-semaphore.o sam_sort-access.o sam_sort-univinterval.o sam_sort-interval.o sam_sort-uintlist.o sam_sort-filestring.o sam_sort-parserange.o sam_sort-iit-read-univ.o sam_sort-iit-read.o sam_sort-samheader.o sam_sort-samread.o sam_sort-bzip2.o sam_sort-getline.o sam_sort-datadir.o sam_sort-getopt.o sam_sort-getopt1.o sam_sort-sam_sort.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-block.o `test -f 'block.c' || echo './'`block.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo './'`chrom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo './'`gregion.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-match.o `test -f 'match.c' || echo './'`match.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo './'`stage1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo './'`diag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo './'`cmet.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo './'`atoi.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo './'`pair.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo './'`stage2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo './'`smooth.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo './'`translation.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo './'`stage3.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-request.o `test -f 'request.c' || echo './'`request.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-result.o `test -f 'result.c' || echo './'`result.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-output.o `test -f 'output.c' || echo './'`output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo './'`chimera.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo './'`gmap.c x86_64-pc-linux-gnu-gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-genome_sites.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-transcript.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-getopt.o gmap_nosimd-getopt1.o gmap_nosimd-gmap.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1879:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1879 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb.c:1883:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1883 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo './'`block.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo './'`chrom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo './'`gregion.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo './'`match.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo './'`stage1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo './'`diag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo './'`cmet.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo './'`atoi.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo './'`pair.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo './'`stage2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo './'`smooth.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo './'`translation.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo './'`stage3.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo './'`request.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo './'`result.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo './'`output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo './'`chimera.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo './'`gmap.c x86_64-pc-linux-gnu-gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-genome_sites.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-transcript.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-getopt.o gmapl_nosimd-getopt1.o gmapl_nosimd-gmap.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c In file included from transcriptome.c:28: transcriptome.c: In function ‘Transcriptome_new’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:132:5: note: in expansion of macro ‘FREAD_INT’ 132 | FREAD_INT(&divint,fp); | ^~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-cigar.o `test -f 'cigar.c' || echo './'`cigar.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-samprint.o `test -f 'samprint.c' || echo './'`samprint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo './'`mapq.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo './'`shortread.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-substring.o `test -f 'substring.c' || echo './'`substring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo './'`junction.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo './'`method.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-ladder.o `test -f 'ladder.c' || echo './'`ladder.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo './'`concordance.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo './'`uintlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo './'`listpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo './'`splice.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo './'`indel.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-intersect.o `test -f 'intersect.c' || echo './'`intersect.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-terminal.o `test -f 'terminal.c' || echo './'`terminal.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo './'`request.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo './'`output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c x86_64-pc-linux-gnu-gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genome128_hr.o gsnap_nosimd-genome128_consec.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-regiondb.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mdprint.o gsnap_nosimd-cigar.o gsnap_nosimd-samprint.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-substring.o gsnap_nosimd-junction.o gsnap_nosimd-transcript.o gsnap_nosimd-method.o gsnap_nosimd-stage3hr.o gsnap_nosimd-ladder.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-maxent.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-intersect.o gsnap_nosimd-kmer-search.o gsnap_nosimd-path-solve.o gsnap_nosimd-extension-search.o gsnap_nosimd-segment-search.o gsnap_nosimd-terminal.o gsnap_nosimd-distant-rna.o gsnap_nosimd-distant-dna.o gsnap_nosimd-uint8table_rh.o gsnap_nosimd-uinttable_rh.o gsnap_nosimd-stage1hr.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-outbuffer.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-getopt.o gsnap_nosimd-getopt1.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo './'`reader.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c In file included from transcriptome.c:28: transcriptome.c: In function ‘Transcriptome_new’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:132:5: note: in expansion of macro ‘FREAD_INT’ 132 | FREAD_INT(&divint,fp); | ^~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-diagonals-heap.o `test -f 'merge-diagonals-heap.c' || echo './'`merge-diagonals-heap.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo './'`merge-uint8.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo './'`merge-diagonals-simd-uint8.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1879:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1879 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb.c:1883:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1883 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo './'`oligo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-cigar.o `test -f 'cigar.c' || echo './'`cigar.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-samprint.o `test -f 'samprint.c' || echo './'`samprint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo './'`mapq.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo './'`shortread.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-substring.o `test -f 'substring.c' || echo './'`substring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo './'`junction.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo './'`transcript.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo './'`method.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-ladder.o `test -f 'ladder.c' || echo './'`ladder.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo './'`concordance.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-maxent.o `test -f 'maxent.c' || echo './'`maxent.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo './'`uint8listpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo './'`listpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo './'`intron.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo './'`splice.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo './'`indel.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-intersect.o `test -f 'intersect.c' || echo './'`intersect.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo './'`intersect-large.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-terminal.o `test -f 'terminal.c' || echo './'`terminal.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo './'`request.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo './'`output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c x86_64-pc-linux-gnu-gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genome128_hr.o gsnapl_nosimd-genome128_consec.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-merge-diagonals-heap.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-regiondb.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mdprint.o gsnapl_nosimd-cigar.o gsnapl_nosimd-samprint.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-substring.o gsnapl_nosimd-junction.o gsnapl_nosimd-transcript.o gsnapl_nosimd-method.o gsnapl_nosimd-stage3hr.o gsnapl_nosimd-ladder.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-maxent.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-intersect.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-segment-search.o gsnapl_nosimd-terminal.o gsnapl_nosimd-distant-rna.o gsnapl_nosimd-distant-dna.o gsnapl_nosimd-uint8table_rh.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-getopt.o gsnapl_nosimd-getopt1.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-block.o `test -f 'block.c' || echo './'`block.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo './'`chrom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo './'`gregion.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-match.o `test -f 'match.c' || echo './'`match.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo './'`stage1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo './'`diag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo './'`cmet.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo './'`atoi.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-pair.o `test -f 'pair.c' || echo './'`pair.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-stage2.o `test -f 'stage2.c' || echo './'`stage2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo './'`smooth.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-translation.o `test -f 'translation.c' || echo './'`translation.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-stage3.o `test -f 'stage3.c' || echo './'`stage3.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-request.o `test -f 'request.c' || echo './'`request.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-result.o `test -f 'result.c' || echo './'`result.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-output.o `test -f 'output.c' || echo './'`output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmap_avx2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c x86_64-pc-linux-gnu-gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-genome_sites.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-transcript.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-getopt.o gmap_avx2-getopt1.o gmap_avx2-gmap.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo './'`md5.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo './'`sequence.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c In file included from compress-write.c:21: compress-write.c: In function ‘Compress_cat’: littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ compress-write.c:877:5: note: in expansion of macro ‘FREAD_UINTS’ 877 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1879:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1879 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb.c:1883:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1883 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-block.o `test -f 'block.c' || echo './'`block.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo './'`chrom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo './'`gregion.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-match.o `test -f 'match.c' || echo './'`match.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo './'`stage1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo './'`diag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo './'`cmet.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo './'`atoi.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo './'`pair.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo './'`stage2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo './'`smooth.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-translation.o `test -f 'translation.c' || echo './'`translation.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-stage3.o `test -f 'stage3.c' || echo './'`stage3.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-request.o `test -f 'request.c' || echo './'`request.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-result.o `test -f 'result.c' || echo './'`result.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-output.o `test -f 'output.c' || echo './'`output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-chimera.o `test -f 'chimera.c' || echo './'`chimera.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gmapl_avx2-gmap.o `test -f 'gmap.c' || echo './'`gmap.c x86_64-pc-linux-gnu-gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-genome_sites.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-transcript.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-getopt.o gmapl_avx2-getopt1.o gmapl_avx2-gmap.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c In file included from transcriptome.c:28: transcriptome.c: In function ‘Transcriptome_new’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:132:5: note: in expansion of macro ‘FREAD_INT’ 132 | FREAD_INT(&divint,fp); | ^~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple’: indexdb.c:1935:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1935 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-cigar.o `test -f 'cigar.c' || echo './'`cigar.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-samprint.o `test -f 'samprint.c' || echo './'`samprint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo './'`mapq.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo './'`shortread.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-substring.o `test -f 'substring.c' || echo './'`substring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo './'`junction.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-method.o `test -f 'method.c' || echo './'`method.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-ladder.o `test -f 'ladder.c' || echo './'`ladder.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo './'`concordance.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo './'`uintlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo './'`listpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo './'`splice.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo './'`indel.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-intersect.o `test -f 'intersect.c' || echo './'`intersect.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-terminal.o `test -f 'terminal.c' || echo './'`terminal.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo './'`uinttable_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-request.o `test -f 'request.c' || echo './'`request.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-output.o `test -f 'output.c' || echo './'`output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnap_avx2-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c x86_64-pc-linux-gnu-gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genome128_hr.o gsnap_avx2-genome128_consec.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-regiondb.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mdprint.o gsnap_avx2-cigar.o gsnap_avx2-samprint.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-substring.o gsnap_avx2-junction.o gsnap_avx2-transcript.o gsnap_avx2-method.o gsnap_avx2-stage3hr.o gsnap_avx2-ladder.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-maxent.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-knownsplicing.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-bitpack64-access.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-intersect.o gsnap_avx2-kmer-search.o gsnap_avx2-path-solve.o gsnap_avx2-extension-search.o gsnap_avx2-segment-search.o gsnap_avx2-terminal.o gsnap_avx2-distant-rna.o gsnap_avx2-distant-dna.o gsnap_avx2-uint8table_rh.o gsnap_avx2-uinttable_rh.o gsnap_avx2-stage1hr.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-outbuffer.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-getopt.o gsnap_avx2-getopt1.o gsnap_avx2-gsnap.o -lz -lbz2 -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-except.o `test -f 'except.c' || echo './'`except.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-assert.o `test -f 'assert.c' || echo './'`assert.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo './'`mem.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo './'`intlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo './'`uint8list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-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:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-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:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint’: bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_write_uint8’: bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ bigendian.c: In function ‘Bigendian_fileio_read_uint8’: bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo './'`interval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo './'`semaphore.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo './'`access.c access.c: In function ‘copy_memory_from_file’: access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:569:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 569 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:574:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 574 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c: In function ‘copy_limited_from_file’: access.c:600:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 600 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:602:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 602 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:608:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:610:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 610 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:616:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 616 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:618:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 618 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:624:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 624 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ access.c:626:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 626 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo './'`filestring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_tree_univ’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1188:2: note: in expansion of macro ‘FREAD_UINT’ 1188 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1190:2: note: in expansion of macro ‘FREAD_INT’ 1190 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1191:2: note: in expansion of macro ‘FREAD_INT’ 1191 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1192:2: note: in expansion of macro ‘FREAD_INT’ 1192 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1193:2: note: in expansion of macro ‘FREAD_INT’ 1193 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_intervals_univ’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1241:7: note: in expansion of macro ‘FREAD_UINT8’ 1241 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1242:7: note: in expansion of macro ‘FREAD_UINT8’ 1242 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1243:7: note: in expansion of macro ‘FREAD_INT’ 1243 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1252:7: note: in expansion of macro ‘FREAD_UINT’ 1252 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1254:7: note: in expansion of macro ‘FREAD_UINT’ 1254 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1256:7: note: in expansion of macro ‘FREAD_INT’ 1256 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ iit-read-univ.c: In function ‘read_words’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1316:3: note: in expansion of macro ‘FREAD_UINT’ 1316 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read-univ.c: In function ‘read_annotations’: iit-read-univ.c:1509:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1509 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1513 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1517:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1517 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1521:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1521 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1525:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1525 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from iit-read-univ.c:12: iit-read-univ.c: In function ‘read_words_debug’: littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read-univ.c:1398:3: note: in expansion of macro ‘FREAD_UINT’ 1398 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ iit-read.c: In function ‘IIT_read’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_tree’: iit-read.c:1760:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1761:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1762:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1763:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1764:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c: In function ‘read_intervals’: iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1892:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | 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:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ iit-read.c: In function ‘read_annotations’: iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | 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:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:3516:5: note: in expansion of macro ‘FREAD_INT’ 3516 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ iit-read.c: In function ‘read_words_debug’: littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo './'`reader.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-compress.o `test -f 'compress.c' || echo './'`compress.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function ‘fill_buffer’: genome.c:10603:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10603 | read(this->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘genomecomp_read_current’: genome.c:464:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 464 | read(this->fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_fill_buffer_simple_alt’: genome.c:10845:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 10845 | read(genomealt->fd,gbuffer1,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_get_char’: genome.c:11014:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11014 | read(this->fd,gbuffer1,/*length*/1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ genome.c: In function ‘Genome_ntcounts’: genome.c:11334:7: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 11334 | read(this->fd,gbuffer,length); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-transcriptome.o `test -f 'transcriptome.c' || echo './'`transcriptome.c In file included from transcriptome.c:28: transcriptome.c: In function ‘Transcriptome_new’: littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ transcriptome.c:132:5: note: in expansion of macro ‘FREAD_INT’ 132 | FREAD_INT(&divint,fp); | ^~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo './'`popcount.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-genome128_consec.o `test -f 'genome128_consec.c' || echo './'`genome128_consec.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-heap.o `test -f 'merge-diagonals-heap.c' || echo './'`merge-diagonals-heap.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo './'`merge-uint8.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo './'`merge-diagonals-simd-uint8.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo './'`merge-uint4.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo './'`merge-diagonals-simd-uint4.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function ‘positions_read_multiple_large’: indexdb.c:1879:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1879 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indexdb.c:1883:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1883 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-regiondb.o `test -f 'regiondb.c' || echo './'`regiondb.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo './'`oligo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-mdprint.o `test -f 'mdprint.c' || echo './'`mdprint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-cigar.o `test -f 'cigar.c' || echo './'`cigar.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-samprint.o `test -f 'samprint.c' || echo './'`samprint.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo './'`mapq.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo './'`fopen.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo './'`shortread.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-substring.o `test -f 'substring.c' || echo './'`substring.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo './'`junction.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo './'`transcript.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo './'`method.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-stage3hr.o `test -f 'stage3hr.c' || echo './'`stage3hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-ladder.o `test -f 'ladder.c' || echo './'`ladder.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo './'`concordance.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo './'`simplepair.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-maxent.o `test -f 'maxent.c' || echo './'`maxent.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo './'`intlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8listpool.o `test -f 'uint8listpool.c' || echo './'`uint8listpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-listpool.o `test -f 'listpool.c' || echo './'`listpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo './'`hitlistpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo './'`intron.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo './'`knownsplicing.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo './'`splice.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo './'`indel.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo './'`bitpack64-access.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-univdiag.o `test -f 'univdiag.c' || echo './'`univdiag.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo './'`univdiagpool.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-sedgesort.o `test -f 'sedgesort.c' || echo './'`sedgesort.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-intersect.o `test -f 'intersect.c' || echo './'`intersect.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo './'`intersect-large.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-kmer-search.o `test -f 'kmer-search.c' || echo './'`kmer-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo './'`path-solve.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-extension-search.o `test -f 'extension-search.c' || echo './'`extension-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-segment-search.o `test -f 'segment-search.c' || echo './'`segment-search.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-terminal.o `test -f 'terminal.c' || echo './'`terminal.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-distant-rna.o `test -f 'distant-rna.c' || echo './'`distant-rna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-distant-dna.o `test -f 'distant-dna.c' || echo './'`distant-dna.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo './'`uint8table_rh.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo './'`stage1hr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo './'`request.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo './'`resulthr.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-output.o `test -f 'output.c' || echo './'`output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-samheader.o `test -f 'samheader.c' || echo './'`samheader.c samheader.c: In function ‘SAM_header_change_HD_tosorted’: samheader.c:196:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 196 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samheader.c:201:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo './'`datadir.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-parserange.o `test -f 'parserange.c' || echo './'`parserange.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-getline.o `test -f 'getline.c' || echo './'`getline.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-getopt.o `test -f 'getopt.c' || echo './'`getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo './'`gsnap.c x86_64-pc-linux-gnu-gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -O2 -pipe -march=native -fno-diagnostics-color -Wformat -Werror=format-security -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genome128_hr.o gsnapl_avx2-genome128_consec.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-merge-diagonals-heap.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-regiondb.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-mdprint.o gsnapl_avx2-cigar.o gsnapl_avx2-samprint.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-substring.o gsnapl_avx2-junction.o gsnapl_avx2-transcript.o gsnapl_avx2-method.o gsnapl_avx2-stage3hr.o gsnapl_avx2-ladder.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-maxent.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-intersect.o gsnapl_avx2-intersect-large.o gsnapl_avx2-kmer-search.o gsnapl_avx2-path-solve.o gsnapl_avx2-extension-search.o gsnapl_avx2-segment-search.o gsnapl_avx2-terminal.o gsnapl_avx2-distant-rna.o gsnapl_avx2-distant-dna.o gsnapl_avx2-uint8table_rh.o gsnapl_avx2-stage1hr.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-outbuffer.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-getopt.o gsnapl_avx2-getopt1.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm make[2]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/src' make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/src' Making all in util make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/util' cp gmap_process.pl gmap_process chmod +x gmap_process cp gmap_build.pl gmap_build chmod +x gmap_build cp gmap_cat.pl gmap_cat chmod +x gmap_cat cp md_coords.pl md_coords chmod +x md_coords cp fa_coords.pl fa_coords chmod +x fa_coords cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites cp psl_introns.pl psl_introns chmod +x psl_introns cp psl_genes.pl psl_genes chmod +x psl_genes cp ensembl_genes.pl ensembl_genes chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/util' Making all in tests make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/tests' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/tests' make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27' make[1]: Nothing to be done for 'all-am'. make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27' >>> Source compiled. >>> Test phase [not enabled]: sci-biology/gmap-2020.10.27 >>> Install sci-biology/gmap-2020.10.27 into /var/tmp/portage/sci-biology/gmap-2020.10.27/image make -j1 DESTDIR=/var/tmp/portage/sci-biology/gmap-2020.10.27/image install Making install in src make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/src' make[2]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/src' /bin/mkdir -p '/var/tmp/portage/sci-biology/gmap-2020.10.27/image/usr/bin' /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex sam_sort gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/var/tmp/portage/sci-biology/gmap-2020.10.27/image/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/src' make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/src' Making install in util make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/util' make[2]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/util' /bin/mkdir -p '/var/tmp/portage/sci-biology/gmap-2020.10.27/image/usr/bin' /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/var/tmp/portage/sci-biology/gmap-2020.10.27/image/usr/bin' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/util' make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/util' Making install in tests make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/tests' make[2]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/tests' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/tests' make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27/tests' make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27' make[2]: Entering directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27' make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2020.10.27/work/gmap-2020-10-27' >>> Completed installing sci-biology/gmap-2020.10.27 into /var/tmp/portage/sci-biology/gmap-2020.10.27/image * Final size of build directory: 221804 KiB (216.6 MiB) * Final size of installed tree: 88564 KiB ( 86.4 MiB) strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/bin/cpuid /usr/bin/gmap /usr/bin/gmapl /usr/bin/get-genome /usr/bin/gmapindex /usr/bin/indexdb_cat /usr/bin/iit_store /usr/bin/iit_get /usr/bin/iit_dump /usr/bin/gsnap /usr/bin/gsnapl /usr/bin/snpindex /usr/bin/cmetindex /usr/bin/atoiindex /usr/bin/trindex /usr/bin/sam_sort /usr/bin/gmap.nosimd /usr/bin/gmapl.nosimd /usr/bin/gsnap.nosimd /usr/bin/gsnapl.nosimd /usr/bin/gmap.avx2 /usr/bin/gmapl.avx2 /usr/bin/gsnap.avx2 /usr/bin/gsnapl.avx2 * checking 46 files for package collisions * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq * owners / ` to identify the installed package that owns a * file. If portageq reports that only one package owns a file then do * NOT file a bug report. A bug report is only useful if it identifies at * least two or more packages that are known to install the same file(s). * If a collision occurs and you can not explain where the file came from * then you should simply ignore the collision since there is not enough * information to determine if a real problem exists. Please do NOT file * a bug report at https://bugs.gentoo.org/ unless you report exactly * which two packages install the same file(s). See * https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how * to solve the problem. And once again, please do NOT file a bug report * unless you have completely understood the above message. * * Detected file collision(s): * * /usr/bin/cpuid * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sys-apps/cpuid-20201006:0::gentoo * /usr/bin/cpuid * * Package 'sci-biology/gmap-2020.10.27' NOT merged due to file * collisions. If necessary, refer to your elog messages for the whole * content of the above message.