sci-biology:gmap-2020.10.27:20201101-203042.log

sci-biology:gmap-2020.10.27:20201101-203042.log (text/plain), 804.85 KB, created by Toralf Förster on 2020-11-01 20:40:33 UTC

 * Package:    sci-biology/gmap-2020.10.27
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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 / <filename>` 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.