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Bug 800617 - sci-libs/io_lib-1.14.14 - /.../ld: ../.../libhtscodecs.a(tokenise_name3.o): relocation R_X86_64_PC32 against symbol tok_key can no
Summary: sci-libs/io_lib-1.14.14 - /.../ld: ../.../libhtscodecs.a(tokenise_name3.o): r...
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 Related Packages
URL:
Whiteboard:
Keywords: PMASKED
Depends on:
Blocks: slibtool
  Show dependency tree
 
Reported: 2021-07-05 07:31 UTC by Toralf Förster
Modified: 2022-08-21 21:32 UTC (History)
0 users

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


Attachments
emerge-info.txt (emerge-info.txt,18.18 KB, text/plain)
2021-07-05 07:31 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,315.20 KB, text/plain)
2021-07-05 07:31 UTC, Toralf Förster
Details
environment (environment,21.48 KB, text/plain)
2021-07-05 07:31 UTC, Toralf Förster
Details
etc.portage.tar.bz2 (etc.portage.tar.bz2,25.62 KB, application/x-bzip)
2021-07-05 07:31 UTC, Toralf Förster
Details
logs.tar.bz2 (logs.tar.bz2,11.91 KB, application/x-bzip)
2021-07-05 07:31 UTC, Toralf Förster
Details
sci-libs:io_lib-1.14.14:20210704-225759.log (sci-libs:io_lib-1.14.14:20210704-225759.log,125.32 KB, text/plain)
2021-07-05 07:31 UTC, Toralf Förster
Details
temp.tar.bz2 (temp.tar.bz2,14.71 KB, application/x-bzip)
2021-07-05 07:31 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2021-07-05 07:31:36 UTC
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../htscodecs/htscodecs/.libs/libhtscodecs.a(rANS_static4x16pr.o): warning: relocation against `rans_key' in read-only section `.text'
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../htscodecs/htscodecs/.libs/libhtscodecs.a(tokenise_name3.o): relocation R_X86_64_PC32 against symbol `tok_key' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
rdlibtool: exec error upon slbt_exec_link_create_library(), line 1572: (see child process error messages).
rdlibtool: < returned to > slbt_exec_link(), line 2084.

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop_plasma_systemd-j3-20210629-092836

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

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 3.9.6
Available Ruby profiles:
  (none found)
Available Rust versions:
  [1]   rust-bin-1.53.0 *
The following VMs are available for generation-2:
1)	IcedTea JDK 3.16.0 [icedtea-bin-8]
*)	AdoptOpenJDK 8.292_p10 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   icedtea-bin-8 
  [2]   openjdk-bin-8  system-vm

The Glorious Glasgow Haskell Compilation System, version 8.10.4
  HEAD of ::gentoo
commit 569d30f949b07f60af1862027633380ec2140ce1
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Sun Jul 4 21:21:27 2021 +0000

    2021-07-04 21:21:26 UTC

emerge -qpvO sci-libs/io_lib
[ebuild  N    ] sci-libs/io_lib-1.14.14  USE="-static-libs"
Comment 1 Toralf Förster gentoo-dev 2021-07-05 07:31:38 UTC
Created attachment 721912 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2021-07-05 07:31:39 UTC
Created attachment 721915 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2021-07-05 07:31:40 UTC
Created attachment 721918 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2021-07-05 07:31:42 UTC
Created attachment 721921 [details]
etc.portage.tar.bz2
Comment 5 Toralf Förster gentoo-dev 2021-07-05 07:31:43 UTC
Created attachment 721924 [details]
logs.tar.bz2
Comment 6 Toralf Förster gentoo-dev 2021-07-05 07:31:44 UTC
Created attachment 721927 [details]
sci-libs:io_lib-1.14.14:20210704-225759.log
Comment 7 Toralf Förster gentoo-dev 2021-07-05 07:31:45 UTC
Created attachment 721930 [details]
temp.tar.bz2
Comment 8 Larry the Git Cow gentoo-dev 2022-07-19 17:11:56 UTC
The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0451c9cd85c8afed7e7dceed9476cd3ffe74b798

commit 0451c9cd85c8afed7e7dceed9476cd3ffe74b798
Author:     Sam James <sam@gentoo.org>
AuthorDate: 2022-07-19 17:08:26 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2022-07-19 17:11:48 +0000

    profiles: last-rite sci-libs/io_lib
    
    Bug: https://bugs.gentoo.org/800617
    Bug: https://bugs.gentoo.org/658318
    Signed-off-by: Sam James <sam@gentoo.org>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)
Comment 9 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2022-07-19 17:12:55 UTC
oh, and it might have bundled htslib. But last rited.
Comment 10 Larry the Git Cow gentoo-dev 2022-08-21 21:32:26 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ff9accf5b259299bf9d5d475fe3f1550500ff39e

commit ff9accf5b259299bf9d5d475fe3f1550500ff39e
Author:     Jakov Smolić <jsmolic@gentoo.org>
AuthorDate: 2022-08-21 21:07:15 +0000
Commit:     Jakov Smolić <jsmolic@gentoo.org>
CommitDate: 2022-08-21 21:30:56 +0000

    sci-libs/io_lib: treeclean
    
    Closes: https://bugs.gentoo.org/800617
    Closes: https://bugs.gentoo.org/658318
    Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>

 profiles/package.mask                |  6 ------
 sci-libs/io_lib/Manifest             |  1 -
 sci-libs/io_lib/io_lib-1.14.7.ebuild | 37 ------------------------------------
 sci-libs/io_lib/metadata.xml         | 17 -----------------
 4 files changed, 61 deletions(-)