Bug 882279

Summary:	sci-biology/hmmer-2.3.2-r5: hmmcalibrate.c:646:3: warning: implicit declaration of function ‘pthread_setconcurrency’ [-Wimplicit-function-declaration]
Product:	Gentoo Linux	Reporter:	Toralf Förster <toralf>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED FIXED
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	870412
Attachments:	emerge-info.txt emerge-history.txt environment etc.portage.tar.bz2 logs.tar.bz2 sci-biology:hmmer-2.3.2-r5:20221120-173030.log

Description Toralf Förster gentoo-dev

2022-11-20 17:38:12 UTC

 *  Please file a bug about this at https://bugs.gentoo.org/
 *  with the maintainer of the package.
 * 
 * ERROR: sci-biology/hmmer-2.3.2-r5::gentoo failed:
 *   install aborted due to severe warnings shown above
 * 
 * Call stack:

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop_gnome_systemd-j4-20221119-142335

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-12 *
clang/llvm (if any):
/usr/lib/llvm/15
15.0.5
Python 3.10.8
Available Ruby profiles:
  (none found)
Available Rust versions:
  [1]   rust-bin-1.65.0 *
The following VMs are available for generation-2:
1)	OpenJDK 17.0.5_p8 [openjdk-17]
*)	Eclipse Temurin JDK 17.0.5_p8 [openjdk-bin-17]
3)	Eclipse Temurin JDK 8.352_p08 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-17 
  [2]   openjdk-bin-8 
  [3]   openjdk-bin-17  system-vm

The Glorious Glasgow Haskell Compilation System, version 9.0.2
php cli (if any):

  HEAD of ::gentoo
commit 3c5108210c082529e63d5db2669c3aa20770425a
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Sun Nov 20 16:16:52 2022 +0000

    2022-11-20 16:16:52 UTC

emerge -qpvO sci-biology/hmmer
[ebuild  N    ] sci-biology/hmmer-3.1_beta2-r1  USE="-gsl -mpi -test" CPU_FLAGS_X86="sse"

Comment 1 Toralf Förster gentoo-dev

2022-11-20 17:38:14 UTC

Created attachment 835107 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2022-11-20 17:38:18 UTC

Created attachment 835109 [details]
emerge-history.txt

Comment 3 Toralf Förster gentoo-dev

2022-11-20 17:38:20 UTC

Created attachment 835111 [details]
environment

Comment 4 Toralf Förster gentoo-dev

2022-11-20 17:38:22 UTC

Created attachment 835113 [details]
etc.portage.tar.bz2

Comment 5 Toralf Förster gentoo-dev

2022-11-20 17:38:23 UTC

Created attachment 835115 [details]
logs.tar.bz2

Comment 6 Toralf Förster gentoo-dev

2022-11-20 17:38:24 UTC

Created attachment 835117 [details]
sci-biology:hmmer-2.3.2-r5:20221120-173030.log

Comment 7 Larry the Git Cow gentoo-dev

2022-11-20 21:23:17 UTC

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

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=41183c48ca86eaaee196abfb18b935f12836f75a

commit 41183c48ca86eaaee196abfb18b935f12836f75a
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2022-11-20 21:23:10 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2022-11-20 21:23:10 +0000

    sci-biology/hmmer: expose XSI pthread_setconcurrency() prototypes
    
    Closes: https://bugs.gentoo.org/882279
    Signed-off-by: David Seifert <soap@gentoo.org>

 sci-biology/hmmer/hmmer-2.3.2-r5.ebuild | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)