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Bug 599232 - sci-biology/arb-5.3 - respect EPREFIX
Summary: sci-biology/arb-5.3 - respect EPREFIX
Status: RESOLVED WONTFIX
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Deadline: 2019-04-30
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords: PMASKED
Depends on:
Blocks:
 
Reported: 2016-11-08 19:31 UTC by Martin Mokrejš
Modified: 2019-05-02 18:46 UTC (History)
2 users (show)

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

Attachments
build.log (build.log,677.03 KB, text/plain)
2016-11-08 19:31 UTC, Martin Mokrejš 		Details
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Description Martin Mokrejš 2016-11-08 19:31:40 UTC 
Created attachment 452742 [details]
build.log

>>> Completed installing arb-5.3 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image/

 * Final size of build directory: 97727 KiB
 * Final size of installed tree: 16280 KiB

 * QA Notice: make jobserver unavailable:
 * 
 *      make[1]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
 *      make[3]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
 *      make[4]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
 *      make[4]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
 *      make[4]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
 * QA Notice: the following files are outside of the prefix:
 * /opt
 * /opt/arb
 * /opt/arb/arb_install.sh
 * /opt/arb/arb_CHANGES.txt
 * /opt/arb/arb_UBUNTU.txt
 * /opt/arb/PERL_SCRIPTS
 * /opt/arb/PERL_SCRIPTS/BIOPERL
 * /opt/arb/PERL_SCRIPTS/BIOPERL/README
 * /opt/arb/PERL_SCRIPTS/BIOPERL/beautifyNewick.pl
 * /opt/arb/PERL_SCRIPTS/GENERAL
 * /opt/arb/PERL_SCRIPTS/GENERAL/listDiff.pl
 * /opt/arb/PERL_SCRIPTS/SAI
 * /opt/arb/PERL_SCRIPTS/SAI/SAI.pm
 * /opt/arb/PERL_SCRIPTS/SAI/SAI_demo.pl
 * /opt/arb/PERL_SCRIPTS/GENOME
 * /opt/arb/PERL_SCRIPTS/GENOME/import_proteomdata.pl
 * /opt/arb/PERL_SCRIPTS/GENOME/GI.pm
 * /opt/arb/PERL_SCRIPTS/test
 * /opt/arb/PERL_SCRIPTS/test/testScripts.pl
 * /opt/arb/PERL_SCRIPTS/test/Makefile
 * /opt/arb/PERL_SCRIPTS/test/test.stamp
 * /opt/arb/PERL_SCRIPTS/ARBTOOLS
 * /opt/arb/PERL_SCRIPTS/ARBTOOLS/raxml2arb.pl
 * /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP
 * /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/format_dssp.pl
 * /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/genbank_gen_long_features.pl
 * /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/embl_gen_long_features.pl
 * /opt/arb/PERL_SCRIPTS/SPECIES
 * /opt/arb/PERL_SCRIPTS/SPECIES/listMarkedSpecies.pl
 * /opt/arb/PERL_SCRIPTS/SPECIES/tools.pm
 * /opt/arb/PERL_SCRIPTS/SPECIES/markSpecies.pl
 * /opt/arb/arb_README.txt
 * /opt/arb/arb_DEBUG.txt
 * /opt/arb/bin
 * /opt/arb/bin/arb_clean
 * /opt/arb/bin/listDiff.pl
 * /opt/arb/bin/retree
 * /opt/arb/bin/format_dssp.pl
 * /opt/arb/bin/arb_dnapars
 * /opt/arb/bin/count
 * /opt/arb/bin/Zuk_to_gen
 * /opt/arb/bin/clustalv
 * /opt/arb/bin/sho_helix
 * /opt/arb/bin/dnaml
 * /opt/arb/bin/fastdnaml
 * /opt/arb/bin/arb_ntree
 * /opt/arb/bin/arb_primer
 * /opt/arb/bin/consense
 * /opt/arb/bin/dolpenny
 * /opt/arb/bin/arb_dist
...
 * ERROR: sci-biology/arb-5.3::gentoo failed:
 *   Aborting due to QA concerns: there are files installed outside the prefix
 * 
 * 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  27:  Called die
 * The specific snippet of code:
 *                      die "Aborting due to QA concerns: there are files installed outside the prefix"
Comment 1 David Seifert gentoo-dev 2017-02-04 21:23:11 UTC 
(In reply to Martin Mokrejš from comment #0)
> Created attachment 452742 [details]
> build.log
> 
> >>> Completed installing arb-5.3 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/arb-5.3/image/
> 
>  * Final size of build directory: 97727 KiB
>  * Final size of installed tree: 16280 KiB
> 
>  * QA Notice: make jobserver unavailable:
>  * 
>  *      make[1]: warning: jobserver unavailable: using -j1.  Add '+' to
> parent make rule.
>  *      make[3]: warning: jobserver unavailable: using -j1.  Add '+' to
> parent make rule.
>  *      make[4]: warning: jobserver unavailable: using -j1.  Add '+' to
> parent make rule.
>  *      make[4]: warning: jobserver unavailable: using -j1.  Add '+' to
> parent make rule.
>  *      make[4]: warning: jobserver unavailable: using -j1.  Add '+' to
> parent make rule.
>  * QA Notice: the following files are outside of the prefix:
>  * /opt
>  * /opt/arb
>  * /opt/arb/arb_install.sh
>  * /opt/arb/arb_CHANGES.txt
>  * /opt/arb/arb_UBUNTU.txt
>  * /opt/arb/PERL_SCRIPTS
>  * /opt/arb/PERL_SCRIPTS/BIOPERL
>  * /opt/arb/PERL_SCRIPTS/BIOPERL/README
>  * /opt/arb/PERL_SCRIPTS/BIOPERL/beautifyNewick.pl
>  * /opt/arb/PERL_SCRIPTS/GENERAL
>  * /opt/arb/PERL_SCRIPTS/GENERAL/listDiff.pl
>  * /opt/arb/PERL_SCRIPTS/SAI
>  * /opt/arb/PERL_SCRIPTS/SAI/SAI.pm
>  * /opt/arb/PERL_SCRIPTS/SAI/SAI_demo.pl
>  * /opt/arb/PERL_SCRIPTS/GENOME
>  * /opt/arb/PERL_SCRIPTS/GENOME/import_proteomdata.pl
>  * /opt/arb/PERL_SCRIPTS/GENOME/GI.pm
>  * /opt/arb/PERL_SCRIPTS/test
>  * /opt/arb/PERL_SCRIPTS/test/testScripts.pl
>  * /opt/arb/PERL_SCRIPTS/test/Makefile
>  * /opt/arb/PERL_SCRIPTS/test/test.stamp
>  * /opt/arb/PERL_SCRIPTS/ARBTOOLS
>  * /opt/arb/PERL_SCRIPTS/ARBTOOLS/raxml2arb.pl
>  * /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP
>  * /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/format_dssp.pl
>  * /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/genbank_gen_long_features.pl
>  * /opt/arb/PERL_SCRIPTS/ARBTOOLS/IFTHELP/embl_gen_long_features.pl
>  * /opt/arb/PERL_SCRIPTS/SPECIES
>  * /opt/arb/PERL_SCRIPTS/SPECIES/listMarkedSpecies.pl
>  * /opt/arb/PERL_SCRIPTS/SPECIES/tools.pm
>  * /opt/arb/PERL_SCRIPTS/SPECIES/markSpecies.pl
>  * /opt/arb/arb_README.txt
>  * /opt/arb/arb_DEBUG.txt
>  * /opt/arb/bin
>  * /opt/arb/bin/arb_clean
>  * /opt/arb/bin/listDiff.pl
>  * /opt/arb/bin/retree
>  * /opt/arb/bin/format_dssp.pl
>  * /opt/arb/bin/arb_dnapars
>  * /opt/arb/bin/count
>  * /opt/arb/bin/Zuk_to_gen
>  * /opt/arb/bin/clustalv
>  * /opt/arb/bin/sho_helix
>  * /opt/arb/bin/dnaml
>  * /opt/arb/bin/fastdnaml
>  * /opt/arb/bin/arb_ntree
>  * /opt/arb/bin/arb_primer
>  * /opt/arb/bin/consense
>  * /opt/arb/bin/dolpenny
>  * /opt/arb/bin/arb_dist
> ...
>  * ERROR: sci-biology/arb-5.3::gentoo failed:
>  *   Aborting due to QA concerns: there are files installed outside the
> prefix
>  * 
>  * 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  27:  Called die
>  * The specific snippet of code:
>  *                      die "Aborting due to QA concerns: there are files
> installed outside the prefix"

arb is completely broken. Please send in a PR with the build system fixes ported and an EAPI 6 ebuild.
Comment 2 Mikle Kolyada (RETIRED) archtester Gentoo Infrastructure gentoo-dev Security 2019-05-02 18:46:03 UTC 
Gone.