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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 packagesAssignee: Gentoo Science Biology related packages <sci-biology>
Status: CONFIRMED ---    
Severity: normal CC: jy6x2b32pie9
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 870412    
Attachments: emerge-info.txt

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/;\
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
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 [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 <>
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]
Comment 2 Toralf Förster gentoo-dev 2022-10-29 09:44:13 UTC
Created attachment 825843 [details]
Comment 3 Toralf Förster gentoo-dev 2022-10-29 09:44:15 UTC
Created attachment 825845 [details]
Comment 4 Toralf Förster gentoo-dev 2022-10-29 09:44:16 UTC
Created attachment 825847 [details]
Comment 5 Toralf Förster gentoo-dev 2022-10-29 09:44:17 UTC
Created attachment 825849 [details]
Comment 6 Toralf Förster gentoo-dev 2022-10-29 09:44:18 UTC
Created attachment 825851 [details]
Comment 7 Toralf Förster gentoo-dev 2022-10-29 09:44:19 UTC
Created attachment 825853 [details]
Comment 8 Toralf Förster gentoo-dev 2022-10-29 09:44:20 UTC
Created attachment 825855 [details]
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.