Bug 715718 – sci-biology/abyss-2.3.4 : Uncompress.cpp: error: redefinition of FILE* fopen(const char*, const char*)

• Status: CONFIRMED
• Product: Gentoo Linux

[Description Toralf Förster 2020-04-01 07:15:00 UTC]

                 from Uncompress.cpp:15:
Uncompress.cpp: At global scope:
Uncompress.cpp:157:7: error: redefinition of FILE* fopen(const char*, const char*)
  157 | FILE *fopen64(const char *path, const char *mode)
      |       ^~~~~~~
Uncompress.cpp:130:7: note: FILE* fopen(const char*, const char*) previously defined here

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.0_musl_hardened-20200328-201618

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

gcc-config -l:
 [1] x86_64-gentoo-linux-musl-9.3.0 *
clang version 10.0.0 
Target: x86_64-gentoo-linux-musl
Thread model: posix
InstalledDir: /usr/lib/llvm/10/bin
/usr/lib/llvm/10
10.0.0
Available Python interpreters, in order of preference:
  [1]   python3.8
  [2]   python3.7
  [3]   python3.6
  [4]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.42.0 *

timestamp of HEAD at this tinderbox image:
/var/db/repos/gentoo	Wed Apr  1 05:37:39 UTC 2020
/var/db/repos/musl	Fri Mar 27 00:25:27 UTC 2020

emerge -qpvO sci-biology/abyss
[ebuild  N    ] sci-biology/abyss-2.0.3  USE="mpi openmp -misc-haskell"

[Comment 1 Toralf Förster 2020-04-01 07:15:03 UTC]

Created attachment 628350 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-04-01 07:15:06 UTC]

Created attachment 628352 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-04-01 07:15:10 UTC]

Created attachment 628354 [details]
environment

[Comment 4 Toralf Förster 2020-04-01 07:15:13 UTC]

Created attachment 628356 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-04-01 07:15:15 UTC]

Created attachment 628358 [details]
logs.tbz2

[Comment 6 Toralf Förster 2020-04-01 07:15:19 UTC]

Created attachment 628360 [details]
sci-biology:abyss-2.0.3:20200401-070520.log

[Comment 7 Toralf Förster 2020-04-01 07:15:22 UTC]

Created attachment 628362 [details]
temp.tbz2

[Comment 8 Larry the Git Cow 2022-01-13 11:21:40 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=89ab6a3d9d32bcb93e27580298094a875a530685

commit 89ab6a3d9d32bcb93e27580298094a875a530685
Author:     Andrew Ammerlaan <[e-mail]>
AuthorDate: 2022-01-13 11:20:26 +0000
Commit:     Andrew Ammerlaan <[e-mail]>
CommitDate: 2022-01-13 11:21:37 +0000

    sci-biology/abyss: drop version 2.0.3
    
    Closes: https://bugs.gentoo.org/741154
    Closes: https://bugs.gentoo.org/715718
    Package-Manager: Portage-3.0.30, Repoman-3.0.3
    Signed-off-by: Andrew Ammerlaan <[e-mail]>

 sci-biology/abyss/Manifest                        |  1 -
 sci-biology/abyss/abyss-2.0.3-r2.ebuild           | 64 -----------------------
 sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch | 11 ----
 3 files changed, 76 deletions(-)

[Comment 9 Toralf Förster 2022-01-13 13:41:41 UTC]

appeared recently at the tinderbox image 17.0_musl-j4-20220111-220013

[Comment 10 Toralf Förster 2022-01-13 13:41:42 UTC]

Created attachment 762083 [details]
emerge-info.txt

[Comment 11 Toralf Förster 2022-01-13 13:41:44 UTC]

Created attachment 762084 [details]
emerge-history.txt

[Comment 12 Toralf Förster 2022-01-13 13:41:45 UTC]

Created attachment 762085 [details]
environment

[Comment 13 Toralf Förster 2022-01-13 13:41:46 UTC]

Created attachment 762086 [details]
etc.portage.tar.bz2

[Comment 14 Toralf Förster 2022-01-13 13:41:47 UTC]

Created attachment 762087 [details]
logs.tar.bz2

[Comment 15 Toralf Förster 2022-01-13 13:41:48 UTC]

Created attachment 762088 [details]
sci-biology:abyss-2.3.4:20220113-131801.log

[Comment 16 Toralf Förster 2022-01-13 13:41:49 UTC]

Created attachment 762089 [details]
temp.tar.bz2

[Comment 17 Agostino Sarubbo 2022-02-04 07:24:30 UTC]

tinderbox_musl has reproduced this issue with version 2.3.4 - Updating summary.