openblas compiles fine, but fails to install with error !!! Error: /var/tmp/portage/sci-libs/openblas-0.2.11/image//etc/env.d/alternatives/blas/openblas-openmp already present. You need ot remove it before adding it again Reproducible: Always emerge --info: Portage 2.2.20 (python 3.4.3-final-0, default/linux/amd64/13.0, gcc-4.9.2, glibc-2.20-r2, 4.0.5 x86_64) ================================================================= System uname: Linux-4.0.5-x86_64-AMD_A8-3870_APU_with_Radeon-tm-_HD_Graphics-with-gentoo-2.2 KiB Mem: 15888956 total, 11263268 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 11 Jun 2015 06:30:02 +0000 sh bash 4.3_p39 ld ld di GNU (Gentoo 2.25 p1.2) 2.25 app-shells/bash: 4.3_p39::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2-r1::gentoo dev-lang/python: 2.7.9-r1::libressl, 3.4.3::gentoo dev-util/cmake: 3.2.3::gentoo dev-util/pkgconfig: 0.28-r3::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.16.4::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r1::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25-r1::gentoo sys-devel/gcc: 4.9.2::gentoo sys-devel/gcc-config: 1.8::gentoo sys-devel/libtool: 2.4.6-r1::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.0::gentoo (virtual/os-headers) sys-libs/glibc: 2.20-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 kernelpanic location: /usr/local/portage masters: gentoo libressl location: /var/lib/layman/libressl sync-type: laymansync sync-uri: https://github.com/gentoo/libressl.git masters: gentoo priority: 50 science location: /var/lib/layman/science sync-type: laymansync sync-uri: https://github.com/gentoo-science/sci.git masters: gentoo priority: 50 tox-overlay location: /var/lib/layman/tox-overlay sync-type: laymansync sync-uri: git://github.com/urras/gentoo-overlay-tox.git masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA @EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -mtune=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/lib64/tomoyo/conf /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -mtune=native -O2 -pipe" DISTDIR="/var/portage/distfiles" FCFLAGS="-march=native -mtune=native -O2 -pipe" FEATURES="assume-digests binpkg-logs clean-logs compress-build-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms split-elog split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-march=native -mtune=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="it_IT.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" USE="3dnow 3dnowext X a52 aac aalib acl alisp alsa amd64 amr ao apng bazaar bluetooth bs2b bzip2 cairo cblas-external cdio chm clang cli colord contrast cracklib crypt cups curl cvs cxx dbus dhcp djbfft djvu dri dri3 dv dvb dvd dvdnav ebook egl emf encode excel exif faac fdk ffmpeg fftw firmware flac fontconfig fontforge fortran fpx ftp gbm gcj gdbm gif gimp gmp gpg gpm graphite gsm gstreamer gudev hdri hwdb iconv icu id3tag inotify int64 ipv6 ipython ithreads jbig jemalloc jpeg jpeg2k kdrive lame lapack latex lcms lensfun libass libcaca libkms libnotify libressl libsamplerate lqr lzma lzo mad matplotlib mercurial metric mmap mmx mmxext mng modplug modules mp3 mp3rtp mpeg mpi multicall multilib multitarget natspec ncurses netlink network nlopt nls nptl numpy obex offensive offlinehelp ogg opencl openexr opengl openmp opus osmesa pam pango passwdqc pcre pdf png pnm popcnt postproc postscript python q16 q32 q64 q8 qt3support quicktime rar raw readline romio rtmp scanner schroedinger secure-delete session smp sndfile sound sox speex sse sse2 sse3 sse4a ssl startup-notification svg system-cairo system-icu system-jpeg system-jsoncpp system-libvpx system-sqlite t1lib tftp tga theora threads tiff timezone truetype twolame type3 udev umfpack unicode usb vcd vdpau vf-dlopen video vim-syntax vorbis vpx wavpack webp wmf wxwidgets x264 x265 xa xdg xephyr xkb xml xmp xorg xpm xscreensaver xv xvfb xvid xvmc yuv4mpeg zlib" ABI_X86="32 64" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext popcnt sse sse2 sse3 sse4a" CURL_SSL="openssl" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="it en" OFFICE_IMPLEMENTATION="libreoffice" OPENMPI_FABRICS="knem" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="aarch64 arm i386 x86_64" QEMU_USER_TARGETS="aarch64 arm i386 x86_64 armeb" RUBY_TARGETS="ruby22" SANE_BACKENDS="plustek" USERLAND="GNU" VIDEO_CARDS="radeon r600" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 404934 [details] complete build log relevant messages * ERROR: sci-libs/openblas-0.2.14::science failed (install phase): * (no error message) * * Call stack: * ebuild.sh, line 93: Called src_install * environment, line 2831: Called multibuild_foreach_variant 'run_in_build_dir' 'fortran-int64_multilib_multibuild_wrapper' 'my_src_install' * environment, line 2015: Called _multibuild_run 'run_in_build_dir' 'fortran-int64_multilib_multibuild_wrapper' 'my_src_install' * environment, line 2013: Called run_in_build_dir 'fortran-int64_multilib_multibuild_wrapper' 'my_src_install' * environment, line 2735: Called fortran-int64_multilib_multibuild_wrapper 'my_src_install' * environment, line 1271: Called my_src_install * environment, line 2811: Called alternatives_for 'blas' 'openblas-openmp' '0' '/usr/lib64/pkgconfig/blas.pc' 'openblas-openmp.pc' * environment, line 546: Called die * The specific snippet of code: * ALTERNATIVESDIR_ROOTLESS="${ED}/etc/env.d/alternatives" eselect alternatives add ${@} || die; * * If you need support, post the output of `emerge --info '=sci-libs/openblas-0.2.14::science'`, * the complete build log and the output of `emerge -pqv '=sci-libs/openblas-0.2.14::science'`. * The complete build log is located at '/var/log/portage/build/sci-libs/openblas-0.2.14:20150611-131128.log.gz'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/openblas-0.2.14/temp/build.log.gz'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/openblas-0.2.14/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/openblas-0.2.14/work/openblas-0.2.14-amd64' * S: '/var/tmp/portage/sci-libs/openblas-0.2.14/work/openblas-0.2.14'
Created attachment 417756 [details] the patch preventing multiple alternative_for calls
This bug is caused because `alternatives_for` is called several times in multilib environment (typically twice: for lib32 and lib64). First call of `alternative_for` successfully creates an alternative for openblas, and second call fails complaining that the alternative openblas already exists. The solution is unify `alternative_for` calls to one call, by aggregating its arguments. With attached patch doing this fix, the problem is solved in my environment.
Sorry I uploaded a different patch (previous attached patch is for lapack, fixing the same problem). I will update the correct patch.
Created attachment 417758 [details] the patch preventing multiple alternative_for calls for open blas This is a correct patch. Though this patch is a bit long since I eliminated unnecessary .pc file search and changed indent level, the fix is fundamentally simple.
(In reply to Shunsuke Shimizu from comment #5) > Created attachment 417758 [details] > the patch preventing multiple alternative_for calls for open blas > > This is a correct patch. > > Though this patch is a bit long since I eliminated unnecessary .pc file > search and changed indent level, the fix is fundamentally simple. Thanks for the patches. But I rewrote the whole eclass. It's nearly finished, Just need to update all ebuild. Expect the work to land until the end of the week.
commit bc36b5406f2bb289a3920ef13d50853a567bc83d Author: Justin Lecher <jlec@gentoo.org> Date: Sat Sep 19 09:14:19 2015 +0200 Large fix of numeric code fortran-int64.eclass code has been splitted into numeric-int64-multibuild.eclass, fortran-2.eclass and numeric.eclass. Gentoo: https://bugs.gentoo.org/show_bug.cgi?id=563292 https://bugs.gentoo.org/show_bug.cgi?id=551764 https://bugs.gentoo.org/show_bug.cgi?id=555302 Github: resolves gentoo-science/sci#438 resolves gentoo-science/sci#443 resolves gentoo-science/sci#447 resolves gentoo-science/sci#450 resolves gentoo-science/sci#467 resolves gentoo-science/sci#492 resolves gentoo-science/sci#507 resolves gentoo-science/sci#508 resolves gentoo-science/sci#522 Signed-off-by: Justin Lecher <jlec@gentoo.org>
I think I just hit this bug trying to emerge openblas-0.2.15. Here is an excerpt from the error: * amd64_int32: running numeric-int64-multibuild_multilib_wrapper pc_file blas openblas * int32: running numeric-int64-multibuild_multilib_wrapper pc_install blas openblas * ACCESS DENIED: mkdir: /etc/env.d/alternatives/blas/openblas-threads mkdir: cannot create directory ‘/etc/env.d/alternatives/blas/openblas-threads’: Permission denied !!! Error: Failed to create /etc/env.d/alternatives/blas/openblas-threads Call stack: * alternatives_do_add (alternatives-common.bash:288) * do_add (alternatives.eselect:147) * check_do (core.bash:24) * do_action (core.bash:105) * main (eselect:309) exiting I'll attach the full log too.
Created attachment 418700 [details] build log of installation failure Build log for installation failure in previous message.
Can you open another bug please? Since this one has been marked "resolved fixed" other dev may be ignoring it. Plus that's a separate issue from the original one and it stems from code we incorporated in the latest commit to provide support for prefix. And of course you don't get access denied on prefix so we missed it when testing. The solution will require some thought.
