Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 829816 - sci-biology/eugene-4.1d - ./getopt.h: error: conflicting declaration of C function int getopt()
Summary: sci-biology/eugene-4.1d - ./getopt.h: error: conflicting declaration of C fun...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo musl team
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2021-12-22 16:08 UTC by Toralf Förster
Modified: 2022-07-07 19:58 UTC (History)
1 user (show)

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


Attachments
emerge-info.txt (emerge-info.txt,14.62 KB, text/plain)
2021-12-22 16:08 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,41.17 KB, text/plain)
2021-12-22 16:08 UTC, Toralf Förster
Details
environment (environment,93.54 KB, text/plain)
2021-12-22 16:09 UTC, Toralf Förster
Details
etc.portage.tar.bz2 (etc.portage.tar.bz2,9.22 KB, application/x-bzip)
2021-12-22 16:09 UTC, Toralf Förster
Details
logs.tar.bz2 (logs.tar.bz2,6.70 KB, application/x-bzip)
2021-12-22 16:09 UTC, Toralf Förster
Details
sci-biology:eugene-4.1d:20211222-152522.log (sci-biology:eugene-4.1d:20211222-152522.log,14.07 KB, text/plain)
2021-12-22 16:09 UTC, Toralf Förster
Details
temp.tar.bz2 (temp.tar.bz2,25.24 KB, application/x-bzip)
2021-12-22 16:09 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2021-12-22 16:08:57 UTC
In file included from Param.h:37,
                 from Prediction.h:32,
                 from DAG.h:26,
                 from EuGene.cc:58:
./getopt.h:104:12: error: conflicting declaration of C function 'int getopt()'
  104 | extern int getopt ();
      |            ^~~~~~

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.0_musl_hardened-j4-20211222-090216

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

gcc-config -l:
 [1] x86_64-gentoo-linux-musl-11.2.1 *
Python 3.9.9
Available Ruby profiles:
  [1]   ruby26 (with Rubygems)
  [2]   ruby27 (with Rubygems)
  [3]   ruby30 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.57.0 *
php cli:

  HEAD of ::gentoo
commit 9c27863fff98482ca59f52ef0bb0d69af4a435d0
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Wed Dec 22 14:51:39 2021 +0000

    2021-12-22 14:51:38 UTC

emerge -qpvO sci-biology/eugene
[ebuild  N    ] sci-biology/eugene-4.1d
Comment 1 Toralf Förster gentoo-dev 2021-12-22 16:08:58 UTC
Created attachment 760078 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2021-12-22 16:08:59 UTC
Created attachment 760079 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2021-12-22 16:09:01 UTC
Created attachment 760080 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2021-12-22 16:09:02 UTC
Created attachment 760081 [details]
etc.portage.tar.bz2
Comment 5 Toralf Förster gentoo-dev 2021-12-22 16:09:03 UTC
Created attachment 760082 [details]
logs.tar.bz2
Comment 6 Toralf Förster gentoo-dev 2021-12-22 16:09:04 UTC
Created attachment 760083 [details]
sci-biology:eugene-4.1d:20211222-152522.log
Comment 7 Toralf Förster gentoo-dev 2021-12-22 16:09:05 UTC
Created attachment 760084 [details]
temp.tar.bz2
Comment 8 Larry the Git Cow gentoo-dev 2022-07-07 19:58:09 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=25a6332f19e64bb862a5543f7453629781b511ce

commit 25a6332f19e64bb862a5543f7453629781b511ce
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2022-07-07 19:56:53 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2022-07-07 19:56:53 +0000

    sci-biology/eugene: update EAPI 6 -> 8
    
    Closes: https://bugs.gentoo.org/829816
    Signed-off-by: David Seifert <soap@gentoo.org>

 .../{eugene-4.1d.ebuild => eugene-4.1d-r1.ebuild}  | 13 ++--
 sci-biology/eugene/files/eugene-3.6-plugins.patch  | 58 ++++++++++-------
 .../eugene/files/eugene-4.1d-portable-getopt.patch | 74 ++++++++++++++++++++++
 3 files changed, 114 insertions(+), 31 deletions(-)