sci-biology:gmap-2015.12.31.5:20200207-005303.log

sci-biology:gmap-2015.12.31.5:20200207-005303.log (text/plain), 64.42 KB, created by Toralf Förster on 2020-02-07 18:19:58 UTC

 * Package:    sci-biology/gmap-2015.12.31.5
 * 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-2015-12-31.v5.tar.gz to /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work
>>> Source unpacked in /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work
>>> Preparing source in /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31 ...
 * econf: updating gmap-2015-12-31/config/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating gmap-2015-12-31/config/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --docdir=/usr/share/doc/gmap-2015.12.31.5 --htmldir=/usr/share/doc/gmap-2015.12.31.5/html --libdir=/usr/lib64
checking package version... 2015-12-31
loading default site script ./config.site
checking CFLAGS... -O2 -pipe -march=native -fno-common
checking MPI_CFLAGS... 
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking bindir... /usr/bin
checking for a working version of perl... /usr/bin/perl
checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed
checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes
checking for mpicc... no
checking for hcc... no
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checking for mpcc... no
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checking for cc... /usr/bin/cc
checking for MPI_Init... no
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checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for ANSI C header files... yes
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checking for objdir... .libs
checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for rint in -lm... yes
checking whether to use MPI_File for input... not specified so enabled by default
checking for pthreads feature... not specified so enabled by default
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
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checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... x86_64-pc-linux-gnu-gcc
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking fcntl.h usability... yes
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checking stddef.h usability... yes
checking stddef.h presence... yes
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checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/types.h... (cached) yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
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checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of off_t... 8
checking for _LARGEFILE_SOURCE value needed for large files... no
checking whether alloca is enabled... not specified so enabled by default
checking for working alloca.h... yes
checking for alloca... yes
checking whether mmap is enabled... not specified so enabled by default
checking for working mmap with MAP_FIXED... yes
checking for working mmap with MAP_VARIABLE... no
checking for MAP_FILE in mmap... yes
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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
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checking for index... yes
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checking for strtoul... yes
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checking for shmat... yes
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checking for semop... yes
checking for struct stat64... no
checking for pagesize via sysconf... yes
checking for pagesize via sysctl... no
checking whether fopen accepts "b" mode... yes
checking whether fopen accepts "t" mode... yes
checking for builtin popcount/clz/ctz features... not specified so enabled by default
checking whether -mpopcnt compiler flag works... 6B8B4567 clz=1 ctz=0 popcount=17 yes
checking for __builtin_popcount... yes
checking for __builtin_clz... yes
checking for __builtin_ctz... yes
checking for bsr instruction in assembly... yes
checking whether sse2 is enabled... not specified so enabled by default
checking compiler is defective and requires an immediate in sse2 shift commands... no
checking whether ssse3 is enabled... not specified so enabled by default
checking whether sse4.1 is enabled... not specified so enabled by default
checking whether sse4.2 is enabled... not specified so enabled by default
checking whether avx is enabled... not specified so enabled by default
checking whether avx2 is enabled... not specified so enabled by default
checking whether simd is enabled... not specified so enabled by default
checking for x86 cpuid 0x00000001 output... 306f2:5100800:7ffefbff:bfebfbff
checking whether mmx is enabled and supported by CPU... yes
checking whether sse is enabled and supported by CPU... yes
checking whether sse2 is enabled and supported by CPU... yes
checking whether sse3 is enabled and supported by CPU... yes
checking whether ssse3 is enabled and supported by CPU... yes
checking whether sse4.1 is enabled and supported by CPU... yes
checking whether sse4.2 is enabled and supported by CPU... yes
checking whether avx is enabled and supported by CPU... yes
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether avx is supported by operating system... yes
checking whether popcnt is enabled and supported by CPU... yes
checking for x86 cpuid 0x80000001 output... 0:0:21:2c100800
checking whether lzcnt is enabled and supported by CPU... yes
checking for x86 cpuid 0x00000007 output... 0:0:0:0
checking whether avx2 is enabled and supported by CPU... no
checking whether bmi1 is enabled and supported by CPU... no
checking whether bmi2 is enabled and supported by CPU... no
checking whether C compiler accepts -mmmx... yes
checking for mmintrin.h header file... yes
checking whether C compiler accepts -msse... yes
checking for xmmintrin.h header file... yes
checking whether C compiler accepts -msse2... yes
checking for emmintrin.h header file... yes
checking whether C compiler accepts -msse3... yes
checking for pmmintrin.h header file... yes
checking whether C compiler accepts -mssse3... yes
checking for tmmintrin.h header file... yes
checking whether C compiler accepts -msse4.1... yes
checking for smmintrin.h header file... yes
checking whether C compiler accepts -msse4.2... yes
checking for nmmintrin.h header file... yes
checking whether C compiler accepts -mavx... yes
checking for immintrin.h header file... yes
checking gmapdb... /usr/share
checking MAX_READLENGTH... 300
checking for zlib support... enabled
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for gzeof in -lz... yes
checking for gzgetc in -lz... yes
checking for gzgets in -lz... yes
checking for gzclose in -lz... yes
checking if zlib package is complete... working
checking for gzbuffer in -lz... yes
checking for bzlib support... enabled
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for BZ2_bzReadOpen in -lbz2... yes
checking for BZ2_bzRead in -lbz2... yes
checking for BZ2_bzReadClose in -lbz2... yes
checking if bzlib package is complete... working
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating mpi/Makefile
config.status: creating util/Makefile
config.status: creating util/gmap_compress.pl
config.status: creating util/gmap_uncompress.pl
config.status: creating util/gmap_process.pl
config.status: creating util/gmap_build.pl
config.status: creating util/gmap_reassemble.pl
config.status: creating util/md_coords.pl
config.status: creating util/fa_coords.pl
config.status: creating util/psl_splicesites.pl
config.status: creating util/psl_introns.pl
config.status: creating util/psl_genes.pl
config.status: creating util/ensembl_genes.pl
config.status: creating util/gtf_splicesites.pl
config.status: creating util/gtf_introns.pl
config.status: creating util/gtf_genes.pl
config.status: creating util/gff3_splicesites.pl
config.status: creating util/gff3_introns.pl
config.status: creating util/gff3_genes.pl
config.status: creating util/dbsnp_iit.pl
config.status: creating util/gvf_iit.pl
config.status: creating util/vcf_iit.pl
config.status: creating tests/Makefile
config.status: creating tests/align.test
config.status: creating tests/coords1.test
config.status: creating tests/setup1.test
config.status: creating tests/iit.test
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
checking Standard compiler and flags to be used... x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common
checking Standard linker flags to be used... 
checking MPI compiler and flags to be used... /usr/bin/cc 
checking MPI linker flags to be used... 
checking pthread compiler flags to be used... -pthread
checking popcnt compiler flags to be used...  -mpopcnt
checking SIMD features available on computer...  mmx sse sse2 sse3 ssse3 sse4.1 sse4.2 avx
checking SIMD compiler flags to be used...  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31 ...
make -j1 
Making all in src
make[1]: Entering directory '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31/src'
make  all-am
make[2]: Entering directory '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31/src'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c
littleendian.c: In function ‘Littleendian_write_char’:
littleendian.c:14:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   14 |   write(fd,buf,1);
      |   ^~~~~~~~~~~~~~~
littleendian.c: In function ‘Littleendian_write_uint’:
littleendian.c:27:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   27 |   write(fd,buf,4);
      |   ^~~~~~~~~~~~~~~
littleendian.c: In function ‘Littleendian_write_uint8’:
littleendian.c:44:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   44 |   write(fd,buf,8);
      |   ^~~~~~~~~~~~~~~
littleendian.c: In function ‘Littleendian_write_uint8_as_uint’:
littleendian.c:57:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   57 |   write(fd,buf,4);
      |   ^~~~~~~~~~~~~~~
littleendian.c:63:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   63 |   write(fd,buf,4);
      |   ^~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c
bigendian.c: In function ‘Bigendian_write_char’:
bigendian.c:16:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
   16 |   write(fd,buf,1);
      |   ^~~~~~~~~~~~~~~
bigendian.c: In function ‘Bigendian_write_uint’:
bigendian.c:176:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  176 |   write(fd,buf,4);
      |   ^~~~~~~~~~~~~~~
bigendian.c: In function ‘Bigendian_fileio_read_uint’:
bigendian.c:260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  260 |   read(fd,buf,4);
      |   ^~~~~~~~~~~~~~
bigendian.c: In function ‘Bigendian_write_uint8’:
bigendian.c:328:3: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  328 |   write(fd,buf,8);
      |   ^~~~~~~~~~~~~~~
bigendian.c: In function ‘Bigendian_fileio_read_uint8’:
bigendian.c:445:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  445 |   read(fd,buf,8);
      |   ^~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c
access.c: In function ‘Access_file_exists_p’:
access.c:71:7: warning: implicit declaration of function ‘stat64’; did you mean ‘stat’? [-Wimplicit-function-declaration]
   71 |   if (stat64(filename,&sb) == 0) {
      |       ^~~~~~
      |       stat
access.c: In function ‘copy_memory_from_file’:
access.c:530:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  530 |       fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:535:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  535 |       fread(p,sizeof(unsigned char),filesize/eltsize - i,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:541:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  541 |       fread(p,sizeof(UINT4),FREAD_BATCH,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  546 |       fread(p,sizeof(UINT4),filesize/eltsize - i,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:552:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  552 |       fread(p,sizeof(UINT8),FREAD_BATCH,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
access.c:557:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  557 |       fread(p,sizeof(UINT8),filesize/eltsize - i,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-filestring.o `test -f 'filestring.c' || echo './'`filestring.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c
In file included from iit-read-univ.c:11:
iit-read-univ.c: In function ‘read_tree_univ’:
littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1035:2: note: in expansion of macro ‘FREAD_UINT’
 1035 |  FREAD_UINT(&uint4,fp);
      |  ^~~~~~~~~~
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1037:2: note: in expansion of macro ‘FREAD_INT’
 1037 |  FREAD_INT(&(new->nodes[i].a),fp);
      |  ^~~~~~~~~
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1038:2: note: in expansion of macro ‘FREAD_INT’
 1038 |  FREAD_INT(&(new->nodes[i].b),fp);
      |  ^~~~~~~~~
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1039:2: note: in expansion of macro ‘FREAD_INT’
 1039 |  FREAD_INT(&(new->nodes[i].leftindex),fp);
      |  ^~~~~~~~~
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1040:2: note: in expansion of macro ‘FREAD_INT’
 1040 |  FREAD_INT(&(new->nodes[i].rightindex),fp);
      |  ^~~~~~~~~
iit-read-univ.c: In function ‘read_intervals_univ’:
littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   25 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1088:7: note: in expansion of macro ‘FREAD_UINT8’
 1088 |       FREAD_UINT8(&(new->intervals[i].low),fp);
      |       ^~~~~~~~~~~
littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   25 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1089:7: note: in expansion of macro ‘FREAD_UINT8’
 1089 |       FREAD_UINT8(&(new->intervals[i].high),fp);
      |       ^~~~~~~~~~~
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1090:7: note: in expansion of macro ‘FREAD_INT’
 1090 |       FREAD_INT(&(new->intervals[i].type),fp);
      |       ^~~~~~~~~
littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1099:7: note: in expansion of macro ‘FREAD_UINT’
 1099 |       FREAD_UINT(&uint4,fp);
      |       ^~~~~~~~~~
littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1101:7: note: in expansion of macro ‘FREAD_UINT’
 1101 |       FREAD_UINT(&uint4,fp);
      |       ^~~~~~~~~~
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1103:7: note: in expansion of macro ‘FREAD_INT’
 1103 |       FREAD_INT(&(new->intervals[i].type),fp);
      |       ^~~~~~~~~
iit-read-univ.c: In function ‘read_words’:
littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1163:3: note: in expansion of macro ‘FREAD_UINT’
 1163 |   FREAD_UINT(&length,fp);
      |   ^~~~~~~~~~
iit-read-univ.c: In function ‘read_annotations’:
iit-read-univ.c:1385:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 1385 |   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 1389 |   read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 1393 |   read(new->fd,new->labels,new->label_length*sizeof(char));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 1397 |   read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 1401 |   read(new->fd,new->annotations,new->annot_length*sizeof(char));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read-univ.c:11:
iit-read-univ.c: In function ‘read_words_debug’:
littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read-univ.c:1245:3: note: in expansion of macro ‘FREAD_UINT’
 1245 |   FREAD_UINT(&length,fp);
      |   ^~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c
In file included from iit-read.c:12:
iit-read.c: In function ‘IIT_read_divint’:
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2312:5: note: in expansion of macro ‘FREAD_INT’
 2312 |     FREAD_INT(&version,fp);
      |     ^~~~~~~~~
iit-read.c: In function ‘IIT_read’:
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2570:5: note: in expansion of macro ‘FREAD_INT’
 2570 |     FREAD_INT(&new->version,fp);
      |     ^~~~~~~~~
iit-read.c: In function ‘read_tree’:
iit-read.c:1623:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1623 |  fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1624:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1624 |  fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1625:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1625 |  fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1626:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1626 |  fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1627:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1627 |  fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c: In function ‘read_intervals’:
iit-read.c:1708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1708 |       fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1709:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1709 |       fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1711:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1711 |  fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1715:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1715 |       fread(&(new->intervals[divno][i].type),sizeof(int),1,fp);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function ‘read_words’:
littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   25 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1820:5: note: in expansion of macro ‘FREAD_UINT8’
 1820 |     FREAD_UINT8(&length8,fp);
      |     ^~~~~~~~~~~
littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1826:5: note: in expansion of macro ‘FREAD_UINT’
 1826 |     FREAD_UINT(&length,fp);
      |     ^~~~~~~~~~
iit-read.c: In function ‘read_annotations’:
iit-read.c:2207:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2207 |     read(new->fd,new->valueorder,new->total_nintervals*sizeof(int));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2211:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2211 |     read(new->fd,new->values,new->value_length*sizeof(char));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2216 |   read(new->fd,new->labelorder,new->total_nintervals*sizeof(int));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2222:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2222 |     read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2227:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2227 |     read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2238:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2238 |   read(new->fd,new->labels,new->label_length*sizeof(char));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2244:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2244 |     read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2249:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2249 |     read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4));
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2260:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 2260 |   read(new->fd,new->annotations,new->annot_length*sizeof(char));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from iit-read.c:12:
iit-read.c: In function ‘IIT_debug’:
littleendian.h:20:25: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   20 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp)
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:2981:5: note: in expansion of macro ‘FREAD_INT’
 2981 |     FREAD_INT(&new->version,fp);
      |     ^~~~~~~~~
iit-read.c: In function ‘read_words_debug’:
littleendian.h:25:27: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   25 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp)
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1964:5: note: in expansion of macro ‘FREAD_UINT8’
 1964 |     FREAD_UINT8(&length8,fp);
      |     ^~~~~~~~~~~
littleendian.h:21:26: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   21 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
iit-read.c:1969:5: note: in expansion of macro ‘FREAD_UINT’
 1969 |     FREAD_UINT(&length,fp);
      |     ^~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c
genome.c: In function ‘fill_buffer’:
genome.c:10582:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
10582 |       read(this->fd,gbuffer1,length);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘genomecomp_read_current’:
genome.c:458:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  458 |   read(this->fd,buffer,4);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_fill_buffer_simple’:
genome.c:10713:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
10713 |       read(this->fd,gbuffer1,length);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_fill_buffer_simple_alt’:
genome.c:10833:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
10833 |       read(genomealt->fd,gbuffer1,length);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_get_char’:
genome.c:11002:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
11002 |       read(this->fd,gbuffer1,/*length*/1);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
genome.c: In function ‘Genome_ntcounts’:
genome.c:11301:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
11301 |       read(this->fd,gbuffer,length);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-popcount.o `test -f 'popcount.c' || echo './'`popcount.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c
indexdb.c: In function ‘positions_read_multiple’:
indexdb.c:1751:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
 1751 |     read(positions_fd,buffer,4);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c
indexdb_hr.c: In function ‘positions_move_absolute’:
indexdb_hr.c:593:55: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘Positionsptr_T’ {aka ‘unsigned int’} [-Wformat=]
  593 |     fprintf(stderr,"Attempted to do lseek on offset %zd*%d=%zd\n",
      |                                                     ~~^
      |                                                       |
      |                                                       long int
      |                                                     %d
  594 |      ptr,(int) sizeof(Univcoord_T),offset);
      |      ~~~                                               
      |      |
      |      Positionsptr_T {aka unsigned int}
indexdb_hr.c: In function ‘positions_read_multiple’:
indexdb_hr.c:624:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result]
  624 |     read(positions_fd,buffer,4);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c
chrom.c: In function ‘Chrom_from_string’:
chrom.c:116:12: warning: comparison between pointer and zero character constant [-Wpointer-compare]
  116 |   while (p != '\0' && *p >= '0' && *p <= '9') {
      |            ^~
chrom.c:116:10: note: did you mean to dereference the pointer?
  116 |   while (p != '\0' && *p >= '0' && *p <= '9') {
      |          ^
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-output.o `test -f 'output.c' || echo './'`output.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c
samheader.c: In function ‘SAM_header_change_HD_tosorted’:
samheader.c:201:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  201 |     fread(buffer,sizeof(char),CHUNK,input);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samheader.c:206:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  206 |     fread(buffer,sizeof(char),headerlen,input);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.     -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c
/bin/sh ../libtool --tag=CC   --mode=link x86_64-pc-linux-gnu-gcc  -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common   -Wl,-O1 -Wl,--as-needed -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-filestring.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o  -lz -lbz2 -lm 
libtool: link: x86_64-pc-linux-gnu-gcc -pthread -mpopcnt -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mavx -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/usr/share\" -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-filestring.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-output.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o  -lz -lbz2 -lm -pthread
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: gmap-dynprog_end.o:(.bss+0x0): multiple definition of `homopolymerp'; gmap-dynprog_single.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:1300: gmap] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31/src'
make[1]: *** [Makefile:1195: all] Error 2
make[1]: Leaving directory '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31/src'
make: *** [Makefile:315: all-recursive] Error 1
 * ERROR: sci-biology/gmap-2015.12.31.5::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/gmap-2015.12.31.5::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/gmap-2015.12.31.5::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:gmap-2015.12.31.5:20200207-005303.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31'
 * S: '/var/tmp/portage/sci-biology/gmap-2015.12.31.5/work/gmap-2015-12-31'