Build log

bwa-0.5.0:20100907-074039.log (text/plain), 9.94 KB, created by Diego Elio Pettenò (RETIRED) on 2010-09-07 11:28:36 UTC

 * CPV:  sci-biology/bwa-0.5.0
 * REPO: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:  elibc_glibc kernel_linux test userland_GNU x86
>>> Unpacking source...
>>> Unpacking bwa-0.5.0.tar.bz2 to /var/tmp/portage/sci-biology/bwa-0.5.0/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bwa-0.5.0/work
>>> Preparing source in /var/tmp/portage/sci-biology/bwa-0.5.0/work/bwa-0.5.0 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bwa-0.5.0/work/bwa-0.5.0 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/bwa-0.5.0/work/bwa-0.5.0 ...
make -j14 
gcc -c -O2 -pipe -DHAVE_PTHREAD   utils.c -o utils.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwt.c -o bwt.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtio.c -o bwtio.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtaln.c -o bwtaln.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtgap.c -o bwtgap.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   is.c -o is.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bntseq.c -o bntseq.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtmisc.c -o bwtmisc.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtindex.c -o bwtindex.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   stdaln.c -o stdaln.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   simple_dp.c -o simple_dp.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwaseqio.c -o bwaseqio.o
make[1]: Entering directory `/var/tmp/portage/sci-biology/bwa-0.5.0/work/bwa-0.5.0'
make[1]: Nothing to be done for `lib'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bwa-0.5.0/work/bwa-0.5.0'
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwase.c -o bwase.o
bwtio.c: In function ‘bwt_restore_bwt’:
bwtio.c:62:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:63:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:64:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c: In function ‘bwt_restore_sa’:
bwtio.c:36:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:38:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:39:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:40:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c:47:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtio.c: In function ‘bwt_dump_sa’:
bwtio.c:21:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtio.c:22:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtio.c:23:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtio.c:24:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtio.c:25:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtio.c: In function ‘bwt_dump_bwt’:
bwtio.c:11:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtio.c:12:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtio.c:13:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
make[1]: Entering directory `/var/tmp/portage/sci-biology/bwa-0.5.0/work/bwa-0.5.0/bwt_gen'
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwt_gen.c -o bwt_gen.o
bwtaln.c: In function ‘bwa_aln_core’:
bwtaln.c:172:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtaln.c:209:10: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtaln.c:210:24: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwa_pac2cspac’:
bwtmisc.c:239:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtmisc.c:241:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwa_pac2cspac_core’:
bwtmisc.c:209:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwa_pac_rev_core’:
bwtmisc.c:171:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c:180:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtmisc.c:182:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwt_pac2bwt’:
bwtmisc.c:72:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwtmisc.c: In function ‘bwa_seq_len’:
bwtmisc.c:51:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -O2 -pipe -DHAVE_PTHREAD   QSufSort.c -o QSufSort.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwape.c -o bwape.o
bntseq.c: In function ‘bns_fasta2bntseq’:
bntseq.c:215:12: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bntseq.c:229:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bntseq.c:233:10: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bntseq.c:236:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bntseq.c: In function ‘bns_restore’:
bntseq.c:98:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:105:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:113:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:122:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bntseq.c:127:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
bwt_gen.c: In function ‘BWTSaveBwtCodeAndOcc’:
bwt_gen.c:1501:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwt_gen.c:1502:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwt_gen.c:1504:8: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result
bwt_gen.c: In function ‘BWTIncConstructFromPacked’:
bwt_gen.c:1416:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwt_gen.c:1432:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwt_gen.c:1447:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -O2 -pipe -DHAVE_PTHREAD   kstring.c -o kstring.o
bwase.c: In function ‘bwa_print_all_hits’:
bwase.c:458:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:465:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:470:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -O2 -pipe -DHAVE_PTHREAD   cs2nt.c -o cs2nt.o
bwase.c: In function ‘bwa_sai2sam_se_core’:
bwase.c:377:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:388:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:393:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c: In function ‘bwa_refine_gapped’:
bwase.c:195:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwase.c:201:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c: In function ‘bwa_sai2sam_pe_core’:
bwape.c:545:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c:546:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c: In function ‘bwa_paired_sw’:
bwape.c:437:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c: In function ‘bwa_cal_pac_pos_pe’:
bwape.c:257:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bwape.c:261:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtsw2_core.c -o bwtsw2_core.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtsw2_main.c -o bwtsw2_main.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwt_lite.c -o bwt_lite.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -O2 -pipe -DHAVE_PTHREAD   main.c -o main.o
bwtsw2_aux.c: In function ‘bsw2_aln’:
bwtsw2_aux.c:517:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
ar -cru libbwtgen.a bwt_gen.o QSufSort.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/bwa-0.5.0/work/bwa-0.5.0/bwt_gen'
gcc -O2 -pipe -DHAVE_PTHREAD  utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen
>>> Source compiled.
>>> Test phase [none]: sci-biology/bwa-0.5.0

>>> Install bwa-0.5.0 into /var/tmp/portage/sci-biology/bwa-0.5.0/image/ category sci-biology
>>> Completed installing bwa-0.5.0 into /var/tmp/portage/sci-biology/bwa-0.5.0/image/

strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/bin/bwa

 * QA Notice: Files built without respecting LDFLAGS have been detected
 *  Please include the following list of files in your report:
 * /usr/bin/bwa

 * Gentoo contact information ...
herds:
    sci-biology
maintainers:
    [e-mail]