Summary: | sci-biology/STAR-2.5.3a : bam_cat.c:(.text+<snip>): undefined reference to bam_hdr_destroy | ||
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Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | mmokrejs, treecleaner |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: |
emerge-info.txt
emerge-history.txt environment etc.portage.tbz2 sci-biology:STAR-2.5.3a:20200805-064032.log temp.tbz2 |
Description
Toralf Förster
2020-08-05 16:12:36 UTC
Created attachment 653258 [details]
emerge-info.txt
Created attachment 653262 [details]
emerge-history.txt
Created attachment 653264 [details]
environment
Created attachment 653266 [details]
etc.portage.tbz2
Created attachment 653268 [details]
sci-biology:STAR-2.5.3a:20200805-064032.log
Created attachment 653270 [details]
temp.tbz2
I assume this explains what needs to be done: http://dev.thep.lu.se/yat/ticket/934 if >=htslib-1.10 is to be used. Or bump to STAR-2.7.6a. Dear treecleaner@: I'm still able to reproduce this issue right now. Since it has not been fixed for a long time, I'd suggest to evaluate if it is the case to remove this package from the tree. Thanks The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3596083589625a3c954deccfdfb899b49a53a131 commit 3596083589625a3c954deccfdfb899b49a53a131 Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org> AuthorDate: 2022-02-19 11:43:23 +0000 Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> CommitDate: 2022-02-19 11:43:23 +0000 sci-biology/STAR: add version 2.7.10a Closes: https://bugs.gentoo.org/696714 Bug: https://bugs.gentoo.org/741152 Bug: https://bugs.gentoo.org/736056 Bug: https://bugs.gentoo.org/716300 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> sci-biology/STAR/Manifest | 1 + sci-biology/STAR/STAR-2.7.10a.ebuild | 41 ++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bcd5ba73fe296ee35a11a3ee96a62a35afa4ac0a commit bcd5ba73fe296ee35a11a3ee96a62a35afa4ac0a Author: David Seifert <soap@gentoo.org> AuthorDate: 2022-05-07 11:01:01 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2022-05-07 11:01:01 +0000 sci-biology/STAR: drop 2.5.3a Closes: https://bugs.gentoo.org/716300 Closes: https://bugs.gentoo.org/736056 Closes: https://bugs.gentoo.org/741152 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/STAR/Manifest | 1 - sci-biology/STAR/STAR-2.5.3a.ebuild | 42 ------- .../STAR/files/STAR-2.5.3a-fix-build-system.patch | 123 --------------------- 3 files changed, 166 deletions(-) |