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Bug 898730 - sci-biology/pysam-0.20.0 fails to compile (CYTHON3-SYSTEM): Cython.Compiler.Errors.CompileError: libcalignedsegment.pyx
Summary: sci-biology/pysam-0.20.0 fails to compile (CYTHON3-SYSTEM): Cython.Compiler.E...
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 Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: cython3-tracker
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Reported: 2023-03-02 08:28 UTC by Agostino Sarubbo
Modified: 2023-04-08 17:53 UTC (History)
0 users

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

Attachments
build.log (build.log,169.17 KB, text/plain)
2023-03-02 08:28 UTC, Agostino Sarubbo 		Details
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Description Agostino Sarubbo gentoo-dev 2023-03-02 08:28:43 UTC 
https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-biology/pysam-0.20.0 fails to compile (CYTHON3-SYSTEM).
Discovered on: amd64 (internal ref: hardened_tinderbox)

NOTE:
(CYTHON3-SYSTEM) in the summary means that the bug was found on a machine that runs dev-python/cython-3 but this bug MAY or MAY NOT BE related to the new version of cython
Comment 1 Agostino Sarubbo gentoo-dev 2023-03-02 08:28:45 UTC 
Created attachment 855580 [details]
build.log

build log and emerge --info
Comment 2 Larry the Git Cow gentoo-dev 2023-04-08 17:53:47 UTC 
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e88f627a3bada9db443b5234ac3fa71c6102c63d

commit e88f627a3bada9db443b5234ac3fa71c6102c63d
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2023-04-08 17:53:38 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2023-04-08 17:53:38 +0000

    sci-biology/pysam: fix build with cython 3
    
    Closes: https://bugs.gentoo.org/898730
    Signed-off-by: David Seifert <soap@gentoo.org>

 .../pysam/files/pysam-0.21.0-cython-3.patch        | 24 ++++++++++++++++++++++
 sci-biology/pysam/pysam-0.21.0.ebuild              |  6 ++++++
 2 files changed, 30 insertions(+)