sci-biology:bwa-0.7.16a:20200125-182142.log

sci-biology:bwa-0.7.16a:20200125-182142.log (text/plain), 8.69 KB, created by Toralf Förster on 2020-01-25 19:07:19 UTC

 * Package:    sci-biology/bwa-0.7.16a
 * 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 bwa-0.7.16a.tar.bz2 to /var/tmp/portage/sci-biology/bwa-0.7.16a/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bwa-0.7.16a/work
>>> Preparing source in /var/tmp/portage/sci-biology/bwa-0.7.16a/work/bwa-0.7.16a ...
 * Applying bwa-0.7.15-Makefile.patch ...
patching file Makefile
Hunk #1 succeeded at 1 with fuzz 2.
Hunk #2 succeeded at 27 (offset 1 line).
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bwa-0.7.16a/work/bwa-0.7.16a ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/bwa-0.7.16a/work/bwa-0.7.16a ...
make -j1 
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  utils.c -o utils.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kthread.c -o kthread.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kstring.c -o kstring.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt.c -o bwt.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bntseq.c -o bntseq.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwa.c -o bwa.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem.c -o bwamem.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem_pair.c -o bwamem_pair.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem_extra.c -o bwamem_extra.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  malloc_wrap.c -o malloc_wrap.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  QSufSort.c -o QSufSort.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_gen.c -o bwt_gen.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  rope.c -o rope.o
rope.c: In function ‘rope_restore_node’:
rope.c:282:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  282 |  fread(&is_bottom, 1, 1, fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:283:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  283 |  fread(&n, 2, 1, fp);
      |  ^~~~~~~~~~~~~~~~~~~
rope.c:291:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  291 |    fread(p[i].c, 8, 6, fp);
      |    ^~~~~~~~~~~~~~~~~~~~~~~
rope.c:292:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  292 |    fread(q, 2, 1, fp);
      |    ^~~~~~~~~~~~~~~~~~
rope.c:293:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  293 |    fread(q + 1, 1, *q, fp);
      |    ^~~~~~~~~~~~~~~~~~~~~~~
rope.c: In function ‘rope_restore’:
rope.c:312:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  312 |  fread(&r->max_nodes, 4, 1, fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:313:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  313 |  fread(&r->block_len, 4, 1, fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  rle.c -o rle.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  is.c -o is.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtindex.c -o bwtindex.o
x86_64-pc-linux-gnu-ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwashm.c -o bwashm.o
bwashm.c: In function ‘bwa_shm_stage’:
bwashm.c:29:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
   29 |  ftruncate(shmid, BWA_CTL_SIZE);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bwashm.c:66:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
   66 |  ftruncate(shmid, idx->l_mem);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwase.c -o bwase.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwaseqio.c -o bwaseqio.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtgap.c -o bwtgap.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtaln.c -o bwtaln.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bamlite.c -o bamlite.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwape.c -o bwape.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kopen.c -o kopen.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  pemerge.c -o pemerge.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  maxk.c -o maxk.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_core.c -o bwtsw2_core.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_main.c -o bwtsw2_main.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_aux.c -o bwtsw2_aux.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_lite.c -o bwt_lite.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_chain.c -o bwtsw2_chain.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  fastmap.c -o fastmap.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_pair.c -o bwtsw2_pair.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  main.c -o main.o
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ./libbwa.a(rope.o):(.rodata+0x30): multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):(.rodata+0x58): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ./libbwa.a(rle.o):(.rodata+0x0): multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):(.rodata+0x58): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:30: bwa] Error 1
 * ERROR: sci-biology/bwa-0.7.16a::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/bwa-0.7.16a::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/bwa-0.7.16a::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:bwa-0.7.16a:20200125-182142.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/bwa-0.7.16a/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/bwa-0.7.16a/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/bwa-0.7.16a/work/bwa-0.7.16a'
 * S: '/var/tmp/portage/sci-biology/bwa-0.7.16a/work/bwa-0.7.16a'