Bug 755092

Summary:	[science overlay] sci-biology/erpin-5.5b : 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
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 logs.tbz2 sci-biology:erpin-5.5b:20201117-161645.log

Description Toralf Förster gentoo-dev

2020-11-17 18:06:22 UTC

make[1]: Entering directory '/var/tmp/portage/sci-biology/erpin-5.5b/work/erpin5.5b.serv/apps'
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color  -I../include -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o erpin erpin.c -L../lib -lrnaIV -lm ; \
echo skipping strip erpin ; \
chmod 755 erpin ;
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/librnaIV.a(io.o):(.bss+0x0): multiple definition of `MainMaskEvals'; /var/tmp/portage/sci-biology/erpin-5.5b/temp/ccTm3mZg.o:(.bss+0x40): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/librnaIV.a(io.o):(.bss+0x20): multiple definition of `MainMaskDetects'; /var/tmp/portage/sci-biology/erpin-5.5b/temp/ccTm3mZg.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)

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Tue Nov 17 03:35:37 PM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-biology/erpin
[ebuild  N    ] sci-biology/erpin-5.5b

Comment 1 Toralf Förster gentoo-dev

2020-11-17 18:06:24 UTC

Created attachment 671935 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2020-11-17 18:06:25 UTC

Created attachment 671938 [details]
emerge-history.txt

Comment 3 Toralf Förster gentoo-dev

2020-11-17 18:06:27 UTC

Created attachment 671941 [details]
environment

Comment 4 Toralf Förster gentoo-dev

2020-11-17 18:06:28 UTC

Created attachment 671944 [details]
etc.portage.tbz2

Comment 5 Toralf Förster gentoo-dev

2020-11-17 18:06:29 UTC

Created attachment 671947 [details]
logs.tbz2

Comment 6 Toralf Förster gentoo-dev

2020-11-17 18:06:31 UTC

Created attachment 671950 [details]
sci-biology:erpin-5.5b:20201117-161645.log

Comment 7 Larry the Git Cow gentoo-dev

2021-02-20 23:26:06 UTC

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

https://gitweb.gentoo.org/proj/sci.git/commit/?id=f8b429d596992ff8426674833a582610562d198e

commit f8b429d596992ff8426674833a582610562d198e
Author:     Jakov Smolic <jakov.smolic@sartura.hr>
AuthorDate: 2021-02-20 21:17:59 +0000
Commit:     Jakov Smolic <jakov.smolic@sartura.hr>
CommitDate: 2021-02-20 21:57:41 +0000

    sci-biology/erpin: Port to EAPI 7
    
    Closes: https://bugs.gentoo.org/755092
    Signed-off-by: Jakov Smolic <jakov.smolic@sartura.hr>

 sci-biology/erpin/erpin-5.5b.ebuild                | 14 +++---
 .../erpin/files/erpin-5.5b-fno-common.patch        | 55 ++++++++++++++++++++++
 2 files changed, 63 insertions(+), 6 deletions(-)