in gentoo prefix "emerge blas-atlas" apparently wants to install stuff into /etc instead of $EPREFIX/etc Here are my symptons: Output of >emerge blas-atlas ... >>> Completed installing blas-atlas-3.9.3 into >>> /local/aamann/gentoo-prefix/var/tmp/portage/sci-libs/blas-atlas-3.9.3/image/local/aamann/gentoo-prefix/ strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment usr/lib/libatlas.so.0.0.0 usr/lib/blas/threaded-atlas/libblas.so.0.0.0 usr/lib/blas/threaded-atlas/libcblas.so.0.0.0 usr/lib/blas/atlas/libblas.so.0.0.0 usr/lib/blas/atlas/libcblas.so.0.0.0 usr/lib/blas/threaded-atlas/libcblas.a usr/lib/blas/threaded-atlas/libblas.a usr/lib/blas/atlas/libcblas.a usr/lib/blas/atlas/libblas.a usr/lib/libatlas.a * QA Notice: the following files are outside of the prefix: * /etc * /etc/env.d * /etc/env.d/cblas * /etc/env.d/cblas/lib * /etc/env.d/cblas/lib/atlas-threads * /etc/env.d/cblas/lib/atlas * /etc/env.d/blas * /etc/env.d/blas/lib * /etc/env.d/blas/lib/atlas-threads * /etc/env.d/blas/lib/atlas * ERROR: sci-libs/blas-atlas-3.9.3 failed: * Aborting due to QA concerns: there are files installed outside the prefix * * Call stack: * misc-functions.sh, line 1410: Called install_qa_check * misc-functions.sh, line 89: Called install_qa_check_prefix * misc-functions.sh, line 589: Called die * The specific snippet of code: * die "Aborting due to QA concerns: there are files installed outside the prefix" * Here the output of >emerge -pqv =sci-libs/blas-atlas-3.9.3 [ebuild N ] sci-libs/blas-atlas-3.9.3 USE="-debug -doc" and the output of >emerge --info =sci-libs/blas-atlas-3.9.3 Portage 2.2.00.14813-prefix (prefix/linux/amd64, gcc-4.2.4, unavailable, 2.6.24.4-64.fc8 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.24.4-64.fc8-x86_64-AMD_Athlon-tm-_64_X2_Dual_Core_Processor_4200+-with-fedora-8-Werewolf Timestamp of tree: Tue, 24 Nov 2009 14:02:19 +0000 app-shells/bash: 4.0_p35 dev-java/java-config: 1.3.7-r1, 2.1.7 dev-lang/python: 2.5.4-r2, 2.6.2-r2 dev-util/cmake: 2.6.2-r1 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.63-r01.1 sys-devel/automake: 1.9.6-r2, 1.10.2-r00.1, 1.11 sys-devel/binutils: 2.19.51.0.1 sys-devel/gcc-config: 1.4.0-r04.6 sys-devel/libtool: 2.2.6a-r00.2 virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="~amd64-linux" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe" DISTDIR="/local/aamann/gentoo-prefix/usr/portage/distfiles" FEATURES="assume-digests collision-protect distlocks fixpackages news parallel-fetch preserve-libs protect-owned sfperms strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="en_IE.UTF-8" LDFLAGS="-Wl,-O1" PKGDIR="/local/aamann/gentoo-prefix/usr/portage/packages" PORTAGE_CONFIGROOT="/local/aamann/gentoo-prefix/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/local/aamann/gentoo-prefix/var/tmp" PORTDIR="/local/aamann/gentoo-prefix/usr/portage" SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix" USE="X amd64 berkdb bzip2 cairo cli cracklib crypt cxx dri fftw fortran gdbm iconv ipv6 latex mmx modules mudflap ncurses nls nptl nptlonly openmp pcre pdf perl pppd prefix python readline reflection session spl sse sse2 ssl sysfs tcpd unicode xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nv r128 radeon savage sis tdfx trident vesa vga via vmware voodoo" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, LINGUAS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY Reproducible: Always
my eselect was to old emerge eselect solved the problem for me. (see also #277849 for a similar issue). Thanks to Michael Yang for the pointer
