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 ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1_desktop-libressl-20200202-131532 ------------------------------------------------------------------- Please see the tracker bug for details. gcc-config -l: [1] x86_64-pc-linux-gnu-9.2.0 * clang: clang version 9.0.1 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/9/bin llvm: 9.0.1 Available Python interpreters, in order of preference: [1] python3.8 [2] python3.6 [3] python3.7 (fallback) [4] python2.7 (fallback) Available Ruby profiles: [1] ruby24 (with Rubygems) [2] ruby25 (with Rubygems) * Available Rust versions: [1] rust-1.41.0 * java-config: The following VMs are available for generation-2: *) IcedTea JDK 3.14.0 [icedtea-bin-8] Available Java Virtual Machines: [1] icedtea-bin-8 system-vm ghc: The Glorious Glasgow Haskell Compilation System, version 8.0.2 repository: ==> /var/db/repos/gentoo/metadata/timestamp.chk <== Thu, 06 Feb 2020 23:27:06 +0000 emerge -qpvO sci-biology/gmap [ebuild N ] sci-biology/gmap-2015.12.31.5
Created attachment 612428 [details] emerge-info.txt
Created attachment 612430 [details] emerge-history.txt
Created attachment 612432 [details] environment
Created attachment 612434 [details] etc.portage.tbz2
Created attachment 612436 [details] logs.tbz2
Created attachment 612438 [details] sci-biology:gmap-2015.12.31.5:20200207-005303.log
Created attachment 612440 [details] temp.tbz2
Probably worth updating to http://research-pub.gene.com/gmap/src/gmap-gsnap-2020-10-14.tar.gz from http://research-pub.gene.com/gmap/ .
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9a8bd40cd638b96b643898fef0a949b4fe313953 commit 9a8bd40cd638b96b643898fef0a949b4fe313953 Author: David Seifert <soap@gentoo.org> AuthorDate: 2020-11-01 18:36:02 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2020-11-01 18:36:02 +0000 sci-biology/gmap: Remove old 2015.12.31.5 Closes: https://bugs.gentoo.org/708626 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/gmap/Manifest | 1 - sci-biology/gmap/gmap-2015.12.31.5.ebuild | 20 -------------------- 2 files changed, 21 deletions(-) Additionally, it has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e44c9cbdd06cfb672155e0d6747d11e955d90dca commit e44c9cbdd06cfb672155e0d6747d11e955d90dca Author: David Seifert <soap@gentoo.org> AuthorDate: 2020-11-01 18:35:59 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2020-11-01 18:35:59 +0000 sci-biology/gmap: Version bump to 2020.10.27 Bug: https://bugs.gentoo.org/708626 Package-Manager: Portage-3.0.8, Repoman-3.0.2 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/gmap/Manifest | 1 + .../gmap/files/gmap-2020.10.27-fno-common.patch | 22 ++++++++++++++++++++++ sci-biology/gmap/gmap-2020.10.27.ebuild | 17 +++++++++++++++++ 3 files changed, 40 insertions(+)
