Bug 878613

Summary:	sci-biology/hmmer-2.3.2-r5 - cp: cannot stat src/hmmalign: No such file or directory
Product:	Gentoo Linux	Reporter:	Toralf Förster <toralf>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED WORKSFORME
Severity:	normal	CC:	jy6x2b32pie9, soap
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:	~arch only
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	870412
Attachments:	emerge-info.txt clang.tar.bz2 emerge-history.txt environment etc.portage.tar.bz2 logs.tar.bz2 sci-biology:hmmer-2.3.2-r5:20221028-235120.log temp.tar.bz2

Description Toralf Förster gentoo-dev

2022-10-29 09:44:12 UTC

mkdir -p /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image/usr/share/man/man1
for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\
   cp src/$file /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image/usr/bin/;\
done
cp: cannot stat 'src/hmmalign': No such file or directory
cp: cannot stat 'src/hmmbuild': No such file or directory
cp: cannot stat 'src/hmmcalibrate': No such file or directory

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_no_multilib_systemd-j4-20221028-160004

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-12 *
clang/llvm (if any):
clang version 15.0.3
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/15/bin
Configuration file: /etc/clang/clang.cfg
/usr/lib/llvm/15
15.0.3
Python 3.10.8
Available Ruby profiles:
  [1]   ruby27 (with Rubygems)
  [2]   ruby31 (with Rubygems) *
Available Rust versions:
  [1]   rust-bin-1.64.0 *
The following VMs are available for generation-2:
1)	Eclipse Temurin JDK 17.0.4.1_p1 [openjdk-bin-17]
*)	Eclipse Temurin JDK 8.345_p01 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm
  [2]   openjdk-bin-17 

The Glorious Glasgow Haskell Compilation System, version 9.0.2
php cli (if any):
GNU Make 4.3

  HEAD of ::gentoo
commit 7cd1beeccdd8ae4cb750e44548665dd91a53826f
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Fri Oct 28 23:01:59 2022 +0000

    2022-10-28 23:01:58 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

2022-10-29 09:44:13 UTC

Created attachment 825841 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2022-10-29 09:44:13 UTC

Created attachment 825843 [details]
clang.tar.bz2

Comment 3 Toralf Förster gentoo-dev

2022-10-29 09:44:15 UTC

Created attachment 825845 [details]
emerge-history.txt

Comment 4 Toralf Förster gentoo-dev

2022-10-29 09:44:16 UTC

Created attachment 825847 [details]
environment

Comment 5 Toralf Förster gentoo-dev

2022-10-29 09:44:17 UTC

Created attachment 825849 [details]
etc.portage.tar.bz2

Comment 6 Toralf Förster gentoo-dev

2022-10-29 09:44:18 UTC

Created attachment 825851 [details]
logs.tar.bz2

Comment 7 Toralf Förster gentoo-dev

2022-10-29 09:44:19 UTC

Created attachment 825853 [details]
sci-biology:hmmer-2.3.2-r5:20221028-235120.log

Comment 8 Toralf Förster gentoo-dev

2022-10-29 09:44:20 UTC

Created attachment 825855 [details]
temp.tar.bz2

Comment 9 NHO 2024-05-08 09:51:10 UTC

Okay, it fails because it's not including pthread in the hmmcalibrate.c
It sets in config.h #define HMMER_THREADS 1
so it should include pthread.h

I can't reproduce this and I can't understand how this situation is even possible barring very damaged system or libc with bad implementation of pthreads.

Comment 10 David Seifert gentoo-dev

2024-11-03 18:06:24 UTC

Can't reproduce