Summary: | [science overlay] sci-biology/pairagon and sci-biology/TransDecoder-2.1.0 - Aborting due to QA concerns: double prefix files installed | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | Martin Mokrejš <mmokrejs> |
Component: | Overlays | Assignee: | Gentoo Science Related Packages <sci> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | perl, prefix |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- |
Description
Martin Mokrejš
2016-07-01 13:13:17 UTC
Same with sci-biology/TransDecoder-2.1.0::science perl_set_version # this is broken and installs into # /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/ # instead of # /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/ insinto ${VENDOR_LIB}/${PN} Another case with:
>>> Completed installing vcftools-0.1.13 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/vcftools-0.1.13/image/
* Final size of build directory: 1516 KiB
* Final size of installed tree: 83 KiB
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/ double prefix
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr double prefix
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr/lib64 double prefix
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr/lib64/perl5 double prefix
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl double prefix
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0 double prefix
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/Vcf.pm double prefix
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/FaSlice.pm double prefix
* QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/VcfStats.pm double prefix
* ERROR: sci-biology/vcftools-0.1.13::science failed:
* Aborting due to QA concerns: double prefix files installed
*
* Call stack:
* misc-functions.sh, line 603: Called install_qa_check
* misc-functions.sh, line 217: Called source 'install_symlink_html_docs'
* 05prefix, line 114: Called install_qa_check_prefix
* 05prefix, line 19: Called die
* The specific snippet of code:
* die "Aborting due to QA concerns: double prefix files installed"
*
* If you need support, post the output of `emerge --info '=sci-biology/vcftools-0.1.13::science'`,
* the complete build log and the output of `emerge -pqv '=sci-biology/vcftools-0.1.13::science'`.
* The complete build log is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/vcftools-0.1.13/temp/build.log'.
* The ebuild environment file is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/vcftools-0.1.13/temp/environment'.
* Working directory: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/vcftools-0.1.13/image/scratch/mmokrejs/gentoo_rap'
* S: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/vcftools-0.1.13/work/vcftools_0.1.13'
!!! post install failed; exiting.
Indeed, this is too deep path:
$ ls -latr /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/vcftools-0.1.13/image/scratch/mmokrejs/gentoo_rap/scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/
total 140
-rw-r--r-- 1 mmokrejs mmokrejs 18147 Jul 31 22:14 VcfStats.pm
-rw-r--r-- 1 mmokrejs mmokrejs 103499 Jul 31 22:14 Vcf.pm
-rw-r--r-- 1 mmokrejs mmokrejs 6731 Jul 31 22:14 FaSlice.pm
drwxr-xr-x 3 mmokrejs mmokrejs 4096 Jul 31 22:14 ..
drwxr-xr-x 2 mmokrejs mmokrejs 4096 Jul 31 22:14 .
$
The IMAGEDIR should be instead: /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/vcftools-0.1.13/image/scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/
The ebuild contains:
EAPI=5
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
...
src_install(){
perl_set_version
dobin cpp/${PN}
insinto ${VENDOR_LIB}
doins perl/*.pm
dobin perl/{fill,vcf}-*
dodoc README.txt
}
Some general, perl-related class issue although exploitable only on Gentoo:RAP and likely also Gentoo:Prefix installations. I don't see these issue on normal Gentoo installations.
perl or prefix devs, please help.
I wonder if it is only me writing wrong ebuild or whether am the only using the perl_set_version thing or what? $ find /apps/gentoo/var/tmp/portage -name build.log | xargs grep 'double prefix files installed' /apps/gentoo/var/tmp/portage/sci-biology/kraken-0.10.5/temp/build.log: * Aborting due to QA concerns: double prefix files installed /apps/gentoo/var/tmp/portage/sci-biology/kraken-0.10.5/temp/build.log: * die "Aborting due to QA concerns: double prefix files installed" /apps/gentoo/var/tmp/portage/sci-biology/pairagon-1.1/temp/build.log: * Aborting due to QA concerns: double prefix files installed /apps/gentoo/var/tmp/portage/sci-biology/pairagon-1.1/temp/build.log: * die "Aborting due to QA concerns: double prefix files installed" /apps/gentoo/var/tmp/portage/sci-biology/glean-1.0.1/temp/build.log: * Aborting due to QA concerns: double prefix files installed /apps/gentoo/var/tmp/portage/sci-biology/glean-1.0.1/temp/build.log: * die "Aborting due to QA concerns: double prefix files installed" /apps/gentoo/var/tmp/portage/sci-biology/RADtools-9999/temp/build.log: * Aborting due to QA concerns: double prefix files installed /apps/gentoo/var/tmp/portage/sci-biology/RADtools-9999/temp/build.log: * die "Aborting due to QA concerns: double prefix files installed" /apps/gentoo/var/tmp/portage/sci-biology/trnascan-se-1.31/temp/build.log: * Aborting due to QA concerns: double prefix files installed /apps/gentoo/var/tmp/portage/sci-biology/trnascan-se-1.31/temp/build.log: * die "Aborting due to QA concerns: double prefix files installed" /apps/gentoo/var/tmp/portage/sci-biology/twinscan-4.1.2-r1/temp/build.log: * Aborting due to QA concerns: double prefix files installed /apps/gentoo/var/tmp/portage/sci-biology/twinscan-4.1.2-r1/temp/build.log: * die "Aborting due to QA concerns: double prefix files installed" /apps/gentoo/var/tmp/portage/sci-biology/weblogo-2.8.2/temp/build.log: * Aborting due to QA concerns: double prefix files installed /apps/gentoo/var/tmp/portage/sci-biology/weblogo-2.8.2/temp/build.log: * die "Aborting due to QA concerns: double prefix files installed" /apps/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/temp/build.log: * Aborting due to QA concerns: double prefix files installed /apps/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/temp/build.log: * die "Aborting due to QA concerns: double prefix files installed" $ commit 539fae1fd1daad0dc762aaa66fcb6fcec4d46bdc Author: David Seifert <soap@gentoo.org> AuthorDate: Thu Sep 7 22:49:10 2017 +0200 Commit: David Seifert <soap@gentoo.org> CommitDate: Thu Sep 7 22:49:10 2017 +0200 sci-biology/TransDecoder: Remove old Package-Manager: Portage-2.3.8, Repoman-2.3.3 commit 6f631fd58c22a7c42ece339ec8d5ead6d53f55fe Author: David Seifert <soap@gentoo.org> AuthorDate: Thu Sep 7 22:47:27 2017 +0200 Commit: David Seifert <soap@gentoo.org> CommitDate: Thu Sep 7 22:47:34 2017 +0200 sci-biology/TransDecoder: Fix double-prefix Closes: https://bugs.gentoo.org/show_bug.cgi?id=587702 Package-Manager: Portage-2.3.8, Repoman-2.3.3 commit 4bc9cc3e0c3601751f67183b64405caf98191ec8 Author: David Seifert <soap@gentoo.org> AuthorDate: Thu Sep 7 22:39:02 2017 +0200 Commit: David Seifert <soap@gentoo.org> CommitDate: Thu Sep 7 22:39:02 2017 +0200 sci-biology/pairagon: Fix double-prefix Closes: https://bugs.gentoo.org/show_bug.cgi?id=587702 Package-Manager: Portage-2.3.8, Repoman-2.3.3 |