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Bug 707158 - sci-biology/vienna-rna-2.1.8 : fails to build with -fno-common or gcc-10
Summary: sci-biology/vienna-rna-2.1.8 : fails to build with -fno-common or gcc-10
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Deadline: 2020-10-09
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords: PMASKED
Depends on:
Blocks: -fno-common 735438
  Show dependency tree
 
Reported: 2020-01-29 17:49 UTC by Toralf Förster
Modified: 2020-10-09 07:24 UTC (History)
1 user (show)

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


Attachments
emerge-info.txt (emerge-info.txt,15.85 KB, text/plain)
2020-01-29 17:50 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,119.32 KB, text/plain)
2020-01-29 17:50 UTC, Toralf Förster
Details
environment (environment,181.42 KB, text/plain)
2020-01-29 17:50 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,12.87 KB, application/x-bzip)
2020-01-29 17:50 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,14.99 KB, application/x-bzip)
2020-01-29 17:50 UTC, Toralf Förster
Details
sci-biology:vienna-rna-2.1.8:20200129-004812.log (sci-biology:vienna-rna-2.1.8:20200129-004812.log,90.10 KB, text/plain)
2020-01-29 17:50 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,49.95 KB, application/x-bzip)
2020-01-29 17:50 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2020-01-29 17:49:57 UTC
      |                       int                                       size_t {aka long unsigned int}
      |                      %ld
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -O2 -pipe -march=native -fno-common -c -o cmdline.o cmdline.c
x86_64-pc-linux-gnu-gcc  -O2 -pipe -march=native -fno-common -fopenmp -L../lib -Wl,-O1 -Wl,--as-needed -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o  -lRNA -lm 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: globals.o:(.bss+0x40): multiple definition of `GAV'; baum.o:(.bss+0x40): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: globals.o:(.bss+0x0): multiple definition of `GTV'; baum.o:(.bss+0x0): first defined here

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_systemd-20200126-201521

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

  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-1.40.0 *
java-config:
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.242_p08 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Tue, 28 Jan 2020 23:46:22 +0000

emerge -qpvO sci-biology/vienna-rna
[ebuild  N    ] sci-biology/vienna-rna-2.1.8  USE="openmp -doc -python -static-libs" PYTHON_TARGETS="python2_7"
Comment 1 Toralf Förster gentoo-dev 2020-01-29 17:50:00 UTC
Created attachment 607576 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-01-29 17:50:03 UTC
Created attachment 607578 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-01-29 17:50:07 UTC
Created attachment 607580 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-01-29 17:50:09 UTC
Created attachment 607582 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-01-29 17:50:12 UTC
Created attachment 607584 [details]
logs.tbz2
Comment 6 Toralf Förster gentoo-dev 2020-01-29 17:50:15 UTC
Created attachment 607586 [details]
sci-biology:vienna-rna-2.1.8:20200129-004812.log
Comment 7 Toralf Förster gentoo-dev 2020-01-29 17:50:18 UTC
Created attachment 607588 [details]
temp.tbz2
Comment 8 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-10-09 07:24:32 UTC
Package removed.