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Bug 755773 - [science overlay] sci-biology/samstat-1.5.1 : fails to build with -fno-common or gcc-10
Summary: [science overlay] sci-biology/samstat-1.5.1 : fails to build with -fno-common...
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 Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: -fno-common
  Show dependency tree
 
Reported: 2020-11-20 15:55 UTC by Toralf Förster
Modified: 2021-02-20 23:26 UTC (History)
1 user (show)

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


Attachments
emerge-info.txt (emerge-info.txt,17.58 KB, text/plain)
2020-11-20 15:55 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,55.06 KB, text/plain)
2020-11-20 15:55 UTC, Toralf Förster
Details
environment (environment,80.50 KB, text/plain)
2020-11-20 15:55 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,16.33 KB, application/x-bzip)
2020-11-20 15:55 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,4.67 KB, application/x-bzip)
2020-11-20 15:55 UTC, Toralf Förster
Details
sci-biology:samstat-1.5.1:20201120-043744.log (sci-biology:samstat-1.5.1:20201120-043744.log,11.47 KB, text/plain)
2020-11-20 15:55 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,21.37 KB, application/x-bzip)
2020-11-20 15:55 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2020-11-20 15:55:04 UTC
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.  -I../lib   -O2 -pipe -march=native -fno-diagnostics-color   -O2 -funroll-loops   -Wall  -std=gnu99  -c -o hmm.o hmm.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.  -I../lib   -O2 -pipe -march=native -fno-diagnostics-color   -O2 -funroll-loops   -Wall  -std=gnu99  -c -o viz.o viz.c
x86_64-pc-linux-gnu-gcc  -O2 -pipe -march=native -fno-diagnostics-color   -O2 -funroll-loops   -Wall  -std=gnu99   -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o samstat interface.o nuc_code.o misc.o main.o io.o hmm.o viz.o -lm -lpthread  /var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1/lib/libks.a 
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: misc.o:(.bss+0x0): multiple definition of `rev_nuc_code'; nuc_code.o:(.bss+0x0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: misc.o:(.bss+0x20): multiple definition of `nuc_code'; nuc_code.o:(.bss+0x20): first defined here

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

  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	Fri Nov 20 04:05:36 AM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-biology/samstat
[ebuild  N    ] sci-biology/samstat-1.5.1
Comment 1 Toralf Förster gentoo-dev 2020-11-20 15:55:05 UTC
Created attachment 673633 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-11-20 15:55:07 UTC
Created attachment 673636 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-11-20 15:55:08 UTC
Created attachment 673639 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-11-20 15:55:09 UTC
Created attachment 673642 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-11-20 15:55:10 UTC
Created attachment 673645 [details]
logs.tbz2
Comment 6 Toralf Förster gentoo-dev 2020-11-20 15:55:12 UTC
Created attachment 673648 [details]
sci-biology:samstat-1.5.1:20201120-043744.log
Comment 7 Toralf Förster gentoo-dev 2020-11-20 15:55:13 UTC
Created attachment 673651 [details]
temp.tbz2
Comment 8 Larry the Git Cow gentoo-dev 2021-02-20 23:26:11 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/proj/sci.git/commit/?id=6bc33b33b7c919869ab6c5f03854f10b8b14a030

commit 6bc33b33b7c919869ab6c5f03854f10b8b14a030
Author:     Jakov Smolic <jakov.smolic@sartura.hr>
AuthorDate: 2021-02-20 20:25:45 +0000
Commit:     Jakov Smolic <jakov.smolic@sartura.hr>
CommitDate: 2021-02-20 21:57:41 +0000

    sci-biology/samstat: Port to EAPI 7
    
    Closes: https://bugs.gentoo.org/755773
    Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr>

 .../samstat/files/samstat-1.5.1-fno-common.patch   | 31 ++++++++++++++++++++++
 sci-biology/samstat/samstat-1.5.1.ebuild           |  9 +++----
 2 files changed, 35 insertions(+), 5 deletions(-)