* Package: sci-biology/bwa-0.7.16a * Repository: gentoo * Maintainer: sci-biology@gentoo.org * 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'