Summary: | sci-biology/transfac-3.2 fails to install because of Segmentation fault during indexing | ||
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Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | mmokrejs, toralf, treecleaner |
Priority: | Normal | Keywords: | PMASKED |
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- |
Description
Juergen Rose
2011-03-31 06:32:14 UTC
In /var/tmp/portage/sci-biology/transfac-3.2/temp/build.log is not more information than in the last posting At line 233 in /var/tmp/portage/sci-biology/transfac-3.2/temp/environment is the function src_install defined as: src_install () { if ! use minimal; then insinto /usr/share/${PN}-${SLOT}; doins *.dat || die; fi; if use emboss; then insinto /usr/share/EMBOSS/data; doins tf* || die; fi } Sorry the last comment was not correct at line 233 is the function src_compile, which is defined as: src_compile () { if use emboss; then echo; einfo "Indexing TRANSFAC for usage with EMBOSS."; EMBOSS_DATA=. tfextract -auto -infile class.dat || die "Indexing TRANSFAC failed."; echo; fi } tfextract belongs to emboss-6.3.1_p4-r1. Reinstalling sci-biology/emboss did not improve the issue. After downgrading to sci-biology/emboss-6.1.0-r1 I could emerge transfac. But after downgrading to sci-biology/emboss-6.1.0-r1 sci-biology/embassy-vienna-1.7.2-r2 does not emerge, because it depends on sci-biology/emboss-6.3.1_p4-r1. emboss-6.3.1 still has some problems. Don't use this on production systems. Ah, I hit the same bug and unfortunately opened bug #401943. But a stacktrace is attached to it. ;-) Before that patch the ebuild to drop the hardcoded "-O2" from configure.in: see bug #393311. still fails here : ----------------------------------------------------------------- This is an unstable amd64 chroot image (named amd64-kde-unstable_20150820-090512) at a hardened host acting as a tinderbox. Portage 2.2.20.1 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/kde, gcc-4.9.3, glibc-2.21-r1, 4.1.4-hardened x86_64) Maybe adding tree-cleaner ? *** Bug 401943 has been marked as a duplicate of this bug. *** *** Bug 587470 has been marked as a duplicate of this bug. *** *** Bug 789612 has been marked as a duplicate of this bug. *** The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8af52d4f38647cbe75086e693c9dc93ea0bd4e2d commit 8af52d4f38647cbe75086e693c9dc93ea0bd4e2d Author: David Seifert <soap@gentoo.org> AuthorDate: 2022-07-11 12:36:18 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2022-07-11 12:36:18 +0000 profiles: last-rite sci-biology/transfac Bug: https://bugs.gentoo.org/361411 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 5 +++++ 1 file changed, 5 insertions(+) The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0c9a8d595bc0e9f73ec77071ff9f5a798e8443b4 commit 0c9a8d595bc0e9f73ec77071ff9f5a798e8443b4 Author: Jakov Smolić <jsmolic@gentoo.org> AuthorDate: 2022-08-09 07:11:00 +0000 Commit: Jakov Smolić <jsmolic@gentoo.org> CommitDate: 2022-08-09 07:11:00 +0000 sci-biology/transfac: treeclean Closes: https://bugs.gentoo.org/361411 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> profiles/package.mask | 5 ---- sci-biology/transfac/Manifest | 1 - sci-biology/transfac/metadata.xml | 16 ----------- sci-biology/transfac/transfac-3.2-r2.ebuild | 42 ----------------------------- 4 files changed, 64 deletions(-) |