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Bug 907971 - sci-biology/bedtools-2.30.0 fails to compile (MUSL-SYSTEM): BamAux.h:10:17: error: int32_t does not name a type
Summary: sci-biology/bedtools-2.30.0 fails to compile (MUSL-SYSTEM): BamAux.h:10:17: e...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2023-06-07 06:54 UTC by Agostino Sarubbo
Modified: 2024-04-25 09:38 UTC (History)
0 users

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

Attachments
build.log (build.log,124.04 KB, text/plain)
2023-06-07 06:54 UTC, Agostino Sarubbo 		Details
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Description Agostino Sarubbo gentoo-dev 2023-06-07 06:54:53 UTC 
https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-biology/bedtools-2.30.0 fails to compile (MUSL-SYSTEM).
Discovered on: amd64 (internal ref: tinderbox_musl)

NOTE:
(MUSL-SYSTEM) in the summary means that bug was found on a machine that runs MUSL libc but this bug MAY or MAY NOT BE related to musl.
Comment 1 Agostino Sarubbo gentoo-dev 2023-06-07 06:54:55 UTC 
Created attachment 863440 [details]
build.log

build log and emerge --info
Comment 2 Larry the Git Cow gentoo-dev 2024-04-25 09:38:02 UTC 
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6659d55f12a3e8b75dbf9545cac23f37ca00bd58

commit 6659d55f12a3e8b75dbf9545cac23f37ca00bd58
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2024-04-25 09:37:47 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2024-04-25 09:37:47 +0000

    sci-biology/bedtools: add 2.31.1
    
    Bug: https://bugs.gentoo.org/881783
    Bug: https://bugs.gentoo.org/907971
    Bug: https://bugs.gentoo.org/929751
    Signed-off-by: David Seifert <soap@gentoo.org>

 sci-biology/bedtools/Manifest                      |   1 +
 sci-biology/bedtools/bedtools-2.31.1.ebuild        |  49 ++++++
 .../files/bedtools-2.31.1-buildsystem.patch        |  84 ++++++++++
 .../bedtools/files/bedtools-2.31.1-includes.patch  | 178 +++++++++++++++++++++
 .../bedtools/files/bedtools-2.31.1-python.patch    |  40 +++++
 5 files changed, 352 insertions(+)