Bug 755779

Summary:	[science overlay] sci-biology/snap-20131129 : fails to build with -fno-common or gcc-10
Product:	Gentoo Linux	Reporter:	Toralf Förster <toralf>
Component:	Current packages	Assignee:	Gentoo Science Related Packages <sci>
Status:	RESOLVED FIXED
Severity:	normal	CC:	sci-biology
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	705764
Attachments:	emerge-info.txt emerge-history.txt environment etc.portage.tbz2 sci-biology:snap-20131129:20201120-062726.log temp.tbz2

Description Toralf Förster gentoo-dev

2020-11-20 15:55:32 UTC

x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c -o zoeTransition.o zoeTransition.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -c -o zoeTrellis.o zoeTrellis.c
x86_64-pc-linux-gnu-gcc -o zoe-loop -O2 -pipe -march=native -fno-diagnostics-color  zoe-loop.o zoeAlignment.o zoeCDS.o zoeCounter.o zoeDNA.o zoeDistribution.o zoeDuration.o zoeFastaFile.o zoeFeature.o zoeFeatureFactory.o zoeFeatureTable.o zoeHMM.o zoeIsochore.o zoeMath.o zoeModel.o zoePhasePref.o zoeProtein.o zoeScanner.o zoeState.o zoeTools.o zoeTransition.o zoeTrellis.o  -lm
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: zoeAlignment.o:(.bss+0x0): multiple definition of `zoeMethod'; zoe-loop.o:(.bss+0x0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: zoeAlignment.o:(.bss+0x8): multiple definition of `zoeConstructor'; zoe-loop.o:(.bss+0x8): 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 05:46:41 AM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-biology/snap
[ebuild  N    ] sci-biology/snap-20131129

Comment 1 Toralf Förster gentoo-dev

2020-11-20 15:55:34 UTC

Created attachment 673672 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2020-11-20 15:55:35 UTC

Created attachment 673675 [details]
emerge-history.txt

Comment 3 Toralf Förster gentoo-dev

2020-11-20 15:55:37 UTC

Created attachment 673678 [details]
environment

Comment 4 Toralf Förster gentoo-dev

2020-11-20 15:55:38 UTC

Created attachment 673681 [details]
etc.portage.tbz2

Comment 5 Toralf Förster gentoo-dev

2020-11-20 15:55:39 UTC

Created attachment 673684 [details]
sci-biology:snap-20131129:20201120-062726.log

Comment 6 Toralf Förster gentoo-dev

2020-11-20 15:55:41 UTC

Created attachment 673687 [details]
temp.tbz2

Comment 7 Larry the Git Cow gentoo-dev

2021-02-20 23:26:08 UTC

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/proj/sci.git/commit/?id=76a7cb736ee17c7acb763b6752049c41a19cbb8b

commit 76a7cb736ee17c7acb763b6752049c41a19cbb8b
Author:     Jakov Smolic <jakov.smolic@sartura.hr>
AuthorDate: 2021-02-15 20:21:41 +0000
Commit:     Jakov Smolic <jakov.smolic@sartura.hr>
CommitDate: 2021-02-20 21:57:41 +0000

    sci-biology/snap: Port to EAPI 7
    
    Closes: https://bugs.gentoo.org/755779
    Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr>

 sci-biology/snap/files/snap-20131129-fno-common.patch | 15 +++++++++++++++
 sci-biology/snap/snap-20131129.ebuild                 | 14 +++++++-------
 2 files changed, 22 insertions(+), 7 deletions(-)