I am trying to fix an ebuild which in genral works fine on a general gentoo installation but fails under Gentoo:RAP (https://wiki.gentoo.org/wiki/Prefix/libc#Synchronize_with_the_RAP_repository) at least because of the EPREFIX being set to '/scratch/mmokrejs/gentoo_rap/'. >>> Install pairagon-1.1 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/pairagon-1.1/image/ category sci-biology >>> Completed installing pairagon-1.1 into /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/pairagon-1.1/image/ * Final size of build directory: 918 KiB * Final size of installed tree: 80 KiB * QA Notice: make jobserver unavailable: * * make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. * 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/pairagon double prefix * QA Notice: scratch/mmokrejs/gentoo_rap///scratch/mmokrejs/gentoo_rap/usr/lib64/perl5/vendor_perl/5.24.0/pairagon/Alignment.pm double prefix * ERROR: sci-biology/pairagon-1.1::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/pairagon-1.1::science'`, * the complete build log and the output of `emerge -pqv '=sci-biology/pairagon-1.1::science'`. * The complete build log is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/pairagon-1.1/temp/build.log'. * The ebuild environment file is located at '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/pairagon-1.1/temp/environment'. * Working directory: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/pairagon-1.1/image/scratch/mmokrejs/gentoo_rap' * S: '/scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/pairagon-1.1/work/pairagon' !!! post install failed; exiting. Please test with sci-biology/pairagon::science to reproduce the problem.
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
