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Bug 736056 - sci-biology/STAR-2.5.3a : bam_cat.c:(.text+<snip>): undefined reference to bam_hdr_destroy
Summary: sci-biology/STAR-2.5.3a : bam_cat.c:(.text+<snip>): undefined reference to ba...
Status: CONFIRMED
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: 2020-08-05 16:12 UTC by Toralf Förster
Modified: 2021-04-14 06:24 UTC (History)
2 users (show)

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


Attachments
emerge-info.txt (emerge-info.txt,15.80 KB, text/plain)
2020-08-05 16:12 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,161.42 KB, text/plain)
2020-08-05 16:12 UTC, Toralf Förster
Details
environment (environment,47.48 KB, text/plain)
2020-08-05 16:12 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,16.15 KB, application/x-bzip)
2020-08-05 16:12 UTC, Toralf Förster
Details
sci-biology:STAR-2.5.3a:20200805-064032.log (sci-biology:STAR-2.5.3a:20200805-064032.log,40.84 KB, text/plain)
2020-08-05 16:12 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,15.64 KB, application/x-bzip)
2020-08-05 16:12 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2020-08-05 16:12:36 UTC
      |                    ^~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: bam_cat.o: in function `bam_cat(int, char* const*, bam_hdr_t const*, char const*)':
bam_cat.c:(.text+0x310): undefined reference to `bam_hdr_destroy'
collect2: error: ld returned 1 exit status
make: *** [Makefile:90: STAR] Error 1
make: Leaving directory '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source'

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_hardened-libressl_abi32+64-20200802-103910

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-10.2.0 *
clang version 10.0.1 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/10/bin
/usr/lib/llvm/10
10.0.1
Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.9 (fallback)
  [3]   python3.8 (fallback)
  [4]   python3.6 (fallback)
  [5]   python2.7 (fallback)
  [6]   pypy3 (fallback)
Available Ruby profiles:
  [1]   ruby25 (with Rubygems) *
Available Rust versions:
  [1]   rust-bin-1.45.2 *
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.265_p01 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

The Glorious Glasgow Haskell Compilation System, version 8.8.4

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Wed Aug  5 06:05:36 AM UTC 2020
/var/db/repos/libressl	Fri Jul 24 09:42:51 PM UTC 2020

emerge -qpvO sci-biology/STAR
[ebuild  N    ] sci-biology/STAR-2.5.3a
Comment 1 Toralf Förster gentoo-dev 2020-08-05 16:12:39 UTC
Created attachment 653258 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-08-05 16:12:42 UTC
Created attachment 653262 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-08-05 16:12:46 UTC
Created attachment 653264 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-08-05 16:12:49 UTC
Created attachment 653266 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-08-05 16:12:51 UTC
Created attachment 653268 [details]
sci-biology:STAR-2.5.3a:20200805-064032.log
Comment 6 Toralf Förster gentoo-dev 2020-08-05 16:12:54 UTC
Created attachment 653270 [details]
temp.tbz2
Comment 7 Martin Mokrejš 2020-10-18 08:02:10 UTC
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.
Comment 8 Agostino Sarubbo gentoo-dev 2021-04-14 06:24:01 UTC
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