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Bug 755533 - [science overlay] sci-biology/salmon-0.10.2 : fails to build with -fno-common or gcc-10
Summary: [science overlay] sci-biology/salmon-0.10.2 : fails to build with -fno-common...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: -fno-common
  Show dependency tree
 
Reported: 2020-11-19 13:10 UTC by Toralf Förster
Modified: 2020-11-21 14:21 UTC (History)
2 users (show)

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


Attachments
emerge-info.txt (emerge-info.txt,16.89 KB, text/plain)
2020-11-19 13:10 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,48.35 KB, text/plain)
2020-11-19 13:10 UTC, Toralf Förster
Details
environment (environment,116.82 KB, text/plain)
2020-11-19 13:10 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,15.79 KB, application/x-bzip)
2020-11-19 13:10 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,16.90 KB, application/x-bzip)
2020-11-19 13:10 UTC, Toralf Förster
Details
sci-biology:salmon-0.10.2:20201119-122742.log.bz2 (sci-biology:salmon-0.10.2:20201119-122742.log.bz2,41.51 KB, application/x-bzip)
2020-11-19 13:10 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,68.86 KB, application/x-bzip)
2020-11-19 13:10 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2020-11-19 13:10:20 UTC
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/salmon-0.10.2/work/salmon-0.10.2/external/install/lib/libbwa.a(bwa.o):/var/tmp/portage/sci-biology/salmon-0.10.2/work/salmon-0.10.2/external/bwa-0.7.12.5/bwa.c:18: multiple definition of `bwa_pg'; CMakeFiles/salmon.dir/SalmonQuantify.cpp.o:(.data.rel.local+0x0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/salmon-0.10.2/work/salmon-0.10.2/external/install/lib/libstaden-read.a(libstaden_read_la-open_trace_file.o): in function `find_file_url':

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_no-multilib-libressl_science-20201116-220441

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-10.2.0 *
/usr/lib/llvm/11
11.0.0
Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.9 (fallback)
  [3]   python3.8 (fallback)
  [4]   python2.7 (fallback)
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.272_p10 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

The Glorious Glasgow Haskell Compilation System, version 8.8.4

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Thu Nov 19 12:05:45 PM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-biology/salmon
[ebuild  N    ] sci-biology/salmon-0.10.2
Comment 1 Toralf Förster gentoo-dev 2020-11-19 13:10:22 UTC
Created attachment 673042 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-11-19 13:10:23 UTC
Created attachment 673045 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-11-19 13:10:25 UTC
Created attachment 673048 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-11-19 13:10:26 UTC
Created attachment 673051 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-11-19 13:10:27 UTC
Created attachment 673054 [details]
logs.tbz2
Comment 6 Toralf Förster gentoo-dev 2020-11-19 13:10:29 UTC
Created attachment 673057 [details]
sci-biology:salmon-0.10.2:20201119-122742.log.bz2
Comment 7 Toralf Förster gentoo-dev 2020-11-19 13:10:30 UTC
Created attachment 673060 [details]
temp.tbz2