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Bug 878613 - sci-biology/hmmer-2.3.2-r5 - cp: cannot stat src/hmmalign: No such file or directory
Summary: sci-biology/hmmer-2.3.2-r5 - cp: cannot stat src/hmmalign: No such file or di...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: c99-porting
  Show dependency tree
 
Reported: 2022-10-29 09:44 UTC by Toralf Förster
Modified: 2022-10-29 09:44 UTC (History)
0 users

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


Attachments
emerge-info.txt (emerge-info.txt,17.71 KB, text/plain)
2022-10-29 09:44 UTC, Toralf Förster
Details
clang.tar.bz2 (clang.tar.bz2,2.46 KB, application/x-bzip)
2022-10-29 09:44 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,67.11 KB, text/plain)
2022-10-29 09:44 UTC, Toralf Förster
Details
environment (environment,62.60 KB, text/plain)
2022-10-29 09:44 UTC, Toralf Förster
Details
etc.portage.tar.bz2 (etc.portage.tar.bz2,7.36 KB, application/x-bzip)
2022-10-29 09:44 UTC, Toralf Förster
Details
logs.tar.bz2 (logs.tar.bz2,8.17 KB, application/x-bzip)
2022-10-29 09:44 UTC, Toralf Förster
Details
sci-biology:hmmer-2.3.2-r5:20221028-235120.log (sci-biology:hmmer-2.3.2-r5:20221028-235120.log,37.08 KB, text/plain)
2022-10-29 09:44 UTC, Toralf Förster
Details
temp.tar.bz2 (temp.tar.bz2,21.41 KB, application/x-bzip)
2022-10-29 09:44 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
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