* CPV: sci-biology/bwa-0.5.0 * REPO: gentoo * Maintainer: weaver@gentoo.org sci-biology@gentoo.org * 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: weaver@gentoo.org