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Bug 707028 - sci-biology/poa-2-r1 : fails to build with -fno-common or gcc-10
Summary: sci-biology/poa-2-r1 : fails to build with -fno-common or gcc-10
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: -fno-common
  Show dependency tree
 
Reported: 2020-01-28 21:20 UTC by Toralf Förster
Modified: 2020-06-21 17:41 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge-info.txt (emerge-info.txt,15.84 KB, text/plain)
2020-01-28 21:20 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,81.18 KB, text/plain)
2020-01-28 21:20 UTC, Toralf Förster
Details
environment (environment,73.89 KB, text/plain)
2020-01-28 21:20 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,12.10 KB, application/x-bzip)
2020-01-28 21:20 UTC, Toralf Förster
Details
sci-biology:poa-2-r1:20200128-210632.log (sci-biology:poa-2-r1:20200128-210632.log,137.45 KB, text/plain)
2020-01-28 21:20 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,23.66 KB, application/x-bzip)
2020-01-28 21:20 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2020-01-28 21:20:00 UTC
rm -f liblpo.a
ar rc liblpo.a black_flag.o seq_util.o fasta_format.o msa_format.o align_lpo2.o align_lpo_po2.o buildup_lpo.o lpo.o heaviest_bundle.o lpo_format.o create_seq.o remove_bundle.o numeric_data.o stringptr.o
ranlib liblpo.a
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o poa align_score.o main.o -lm liblpo.a
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x0): multiple definition of `Program_version'; align_score.o:(.bss+0x0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x8): multiple definition of `Program_name'; align_score.o:(.bss+0x8): first defined here

  -------------------------------------------------------------------

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop_plasma-libressl-20200126-092715

  -------------------------------------------------------------------

  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]   python3.7 (uninstalled)
  [3]   python3.6
  [4]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.40.0 *
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

repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Tue, 28 Jan 2020 19:46:19 +0000

emerge -qpvO sci-biology/poa
[ebuild  N    ] sci-biology/poa-2-r1  USE="-static-libs"
Comment 1 Toralf Förster gentoo-dev 2020-01-28 21:20:02 UTC
Created attachment 607228 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-01-28 21:20:05 UTC
Created attachment 607230 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-01-28 21:20:08 UTC
Created attachment 607232 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-01-28 21:20:10 UTC
Created attachment 607234 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-01-28 21:20:13 UTC
Created attachment 607236 [details]
sci-biology:poa-2-r1:20200128-210632.log
Comment 6 Toralf Förster gentoo-dev 2020-01-28 21:20:17 UTC
Created attachment 607240 [details]
temp.tbz2
Comment 7 Larry the Git Cow gentoo-dev 2020-06-21 17:41:22 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8674063d381e616d093806be74b00c64fe5b5c81

commit 8674063d381e616d093806be74b00c64fe5b5c81
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2020-06-21 17:40:49 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2020-06-21 17:40:49 +0000

    sci-biology/poa: Fix building against GCC 10
    
    Closes: https://bugs.gentoo.org/707028
    Package-Manager: Portage-2.3.101, Repoman-2.3.22
    Signed-off-by: David Seifert <soap@gentoo.org>

 sci-biology/poa/files/poa-2-fno-common.patch | 13 +++++++++++++
 sci-biology/poa/poa-2-r1.ebuild              |  1 +
 2 files changed, 14 insertions(+)