Created attachment 438664 [details] build.log Hi, I tried to investigate this but I cannot find a proper way to fix either of these. I have a patch: the configure lines show wrong paths but it seems to do the right thing - install binaries and manual pages in proper location. On the other hand, I fear the -Rpath will be wrong ... and binaries will not work. So, I leave it up to somebody more skilled. There are two issues IMHO. First, the ebuild is partially ignoring EPREFIX, probably because of the "emake DESTDIR=...." line in current ebuild: * QA Notice: the following files are outside of the prefix: * /usr * /usr/share * /usr/share/man * /usr/share/man/man1 * /usr/share/man/man1/hmmer.1 * /usr/share/man/man1/hmmpfam.1 * /usr/share/man/man1/hmmalign.1 * /usr/share/man/man1/hmmconvert.1 * /usr/share/man/man1/hmmcalibrate.1 * /usr/share/man/man1/hmmbuild.1 * /usr/share/man/man1/hmmemit.1 * /usr/share/man/man1/hmmindex.1 * /usr/share/man/man1/hmmfetch.1 * /usr/share/man/man1/hmmsearch.1 * /usr/bin * /usr/bin/hmmconvert * /usr/bin/hmmindex * /usr/bin/hmmemit * /usr/bin/hmmalign * /usr/bin/hmmsearch * /usr/bin/hmmpfam * /usr/bin/hmmbuild * /usr/bin/hmmcalibrate * /usr/bin/hmmfetch * ERROR: sci-biology/hmmer-2.3.2-r3::gentoo_prefix failed: * Aborting due to QA concerns: there are files installed outside the prefix * * Call stack: * misc-functions.sh, line 1236: Called install_qa_check * misc-functions.sh, line 223: Called source 'install_symlink_html_docs' * 05prefix, line 115: 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" Second, the configure scripts are served with duplicated --prefix (I show only the latter here). configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: creating src/config.h configure: configuring in squid configure: running /scratch/mmokrejs/gentoo/bin/bash './configure' --prefix=/scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/hmmer-2.3.2-r3/image//usr '--prefix=/scratch/mmokrejs/gentoo/usr' '--build=x86_64-pc-linux-gnu' '--mandir=/scratch/mmokrejs/gentoo/usr/share/man' '--infodir=/scratch/mmokrejs/gentoo/usr/share/info' '--datadir=/scratch/mmokrejs/gentoo/usr/share' '--sysconfdir=/scratch/mmokrejs/gentoo/etc' '--localstatedir=/scratch/mmokrejs/gentoo/var/lib' '--libdir=/scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/hmmer-2.3.2-r3/image/usr/lib' '--host=x86_64-pc-linux-gnu' '--prefix=/scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/hmmer-2.3.2-r3/image//usr' '--exec_prefix=/scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/hmmer-2.3.2-r3/image//usr' '--mandir=/scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/hmmer-2.3.2-r3/image//usr/share/man' '--enable-lfs' '--disable-threads' 'CFLAGS=-O2 -pipe -O2 -pipe -march=native' 'LDFLAGS=-Wl,-O1' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' --cache-file=/dev/null --srcdir=.
Created attachment 438668 [details, diff] hmmer-2.3.2-r3.ebuild.patch
To reproduce from https://wiki.gentoo.org/wiki/Prefix/libc follow a link to http://dev.gentoo.org/~heroxbd/bootstrap-rap.sh and just run it as: export GENTOO_MIRRORS="http://gentoo.mirror.dkm.cz/pub/gentoo/" export EPREFIX="/scratch/mmokrejs/gentoo_rap" bash bootstrap-rap.sh /scratch/mmokrejs/gentoo_rap/startprefix # inside prefixed Gentoo execute the following # emerge app-portage/emerge-delta-webrsync emerge-webrsync # emerge cpuinfo2cpuflags emerge layman layman -a science emerge hmmer
(In reply to Martin Mokrejš from comment #0) > Created attachment 438664 [details] > build.log > > Hi, > I tried to investigate this but I cannot find a proper way to fix either > of these. I have a patch: the configure lines show wrong paths but it seems > to do the right thing - install binaries and manual pages in proper > location. On the other hand, I fear the -Rpath will be wrong ... and > binaries will not work. So, I leave it up to somebody more skilled. I think the patch is fine.
I've tested it by exporting EPREFIX and it seemed to fully respect EPREFIX in src_install(). commit 895b3abfbdacf52dbd7a0e817eb7ebf101ce55a7 Author: David Seifert <soap@gentoo.org> Date: Sun Oct 9 16:52:52 2016 +0200 sci-biology/hmmer: Properly SLOT=2 hmmer-2.3.2 Gentoo-bug: 328911, 586960 * EAPI=6 * Introduce SLOT=2 and rename binaries and static libraries
