Bug 708626 – sci-biology/gmap-2015.12.31.5 : fails to build with -fno-common or gcc-10

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2020-02-07 18:19:41 UTC]

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

[Comment 1 Toralf Förster 2020-02-07 18:19:44 UTC]

Created attachment 612428 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-02-07 18:19:46 UTC]

Created attachment 612430 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-02-07 18:19:49 UTC]

Created attachment 612432 [details]
environment

[Comment 4 Toralf Förster 2020-02-07 18:19:52 UTC]

Created attachment 612434 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-02-07 18:19:55 UTC]

Created attachment 612436 [details]
logs.tbz2

[Comment 6 Toralf Förster 2020-02-07 18:19:58 UTC]

Created attachment 612438 [details]
sci-biology:gmap-2015.12.31.5:20200207-005303.log

[Comment 7 Toralf Förster 2020-02-07 18:20:00 UTC]

Created attachment 612440 [details]
temp.tbz2

[Comment 8 Martin Mokrejš 2020-10-18 08:06:32 UTC]

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/ .

[Comment 9 Larry the Git Cow 2020-11-01 18:36:53 UTC]

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 <[e-mail]>
AuthorDate: 2020-11-01 18:36:02 +0000
Commit:     David Seifert <[e-mail]>
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 <[e-mail]>

 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 <[e-mail]>
AuthorDate: 2020-11-01 18:35:59 +0000
Commit:     David Seifert <[e-mail]>
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 <[e-mail]>

 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(+)