Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 789612 - sci-biology/transfac-3.2-r1 - /.../environment:line <snip>: <snip> Segmentation fault EMBOSS_DATA=. tfextract -auto -infile class.
Summary: sci-biology/transfac-3.2-r1 - /.../environment:line <snip>: <snip> Segmentati...
Status: RESOLVED DUPLICATE of bug 361411
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:
 
Reported: 2021-05-12 09:02 UTC by Toralf Förster
Modified: 2022-07-07 19:21 UTC (History)
0 users

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

Attachments
emerge-info.txt (emerge-info.txt,16.69 KB, text/plain)
2021-05-12 09:02 UTC, Toralf Förster 		Details
emerge-history.txt (emerge-history.txt,130.34 KB, text/plain)
2021-05-12 09:02 UTC, Toralf Förster 		Details
environment (environment,15.54 KB, text/plain)
2021-05-12 09:03 UTC, Toralf Förster 		Details
etc.portage.tar.bz2 (etc.portage.tar.bz2,14.40 KB, application/x-bzip)
2021-05-12 09:03 UTC, Toralf Förster 		Details
logs.tar.bz2 (logs.tar.bz2,936 bytes, application/x-bzip)
2021-05-12 09:03 UTC, Toralf Förster 		Details
sci-biology:transfac-3.2-r1:20210511-215616.log (sci-biology:transfac-3.2-r1:20210511-215616.log,1.90 KB, text/plain)
2021-05-12 09:03 UTC, Toralf Förster 		Details
View All Add an attachment (proposed patch, testcase, etc.)

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2021-05-12 09:02:56 UTC 
 * 
 * Indexing TRANSFAC for usage with EMBOSS
/var/tmp/portage/sci-biology/transfac-3.2-r1/temp/environment: line 366:    34 Segmentation fault      EMBOSS_DATA="." tfextract -auto -infile class.dat
 * ERROR: sci-biology/transfac-3.2-r1::gentoo failed (compile phase):
 *   Indexing TRANSFAC failed
 * 
 * Call stack:

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_hardened-j2-20210510-165205

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-11.1.0 *
clang version 12.0.0
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/12/bin
/usr/lib/llvm/12
12.0.0
Python 3.8.10
Available Rust versions:
  [1]   rust-bin-1.52.1 *
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.292_p10 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

The Glorious Glasgow Haskell Compilation System, version 8.10.4

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Mon May 10 19:50:37 UTC 2021

emerge -qpvO sci-biology/transfac
[ebuild  N    ] sci-biology/transfac-3.2-r1  USE="emboss -minimal"
Comment 1 Toralf Förster gentoo-dev 2021-05-12 09:02:57 UTC 
Created attachment 707298 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2021-05-12 09:02:59 UTC 
Created attachment 707301 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2021-05-12 09:03:00 UTC 
Created attachment 707304 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2021-05-12 09:03:01 UTC 
Created attachment 707307 [details]
etc.portage.tar.bz2
Comment 5 Toralf Förster gentoo-dev 2021-05-12 09:03:02 UTC 
Created attachment 707310 [details]
logs.tar.bz2
Comment 6 Toralf Förster gentoo-dev 2021-05-12 09:03:03 UTC 
Created attachment 707313 [details]
sci-biology:transfac-3.2-r1:20210511-215616.log
Comment 7 David Seifert gentoo-dev 2022-07-07 19:21:24 UTC 

*** This bug has been marked as a duplicate of bug 361411 ***