Created attachment 393048 [details] emerge log x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -Wl,-O1 -Wl,--as-needed -o PathConsensus PathConsensus-PathConsensus.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build/MergePaths' Making all in Misc make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build/Misc' ghc --make -O2 -hidir ./ -odir ./ -o abyss-samtobreak /var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6/Misc/samtobreak.hs /var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6/Misc/samtobreak.hs:16:8: Could not find module ‘System.IO.MMap’ Perhaps you meant System.IO.UTF8 (from utf8-string-0.3.8) Use -v to see a list of the files searched for. Makefile:535: recipe for target 'abyss-samtobreak' failed make[2]: *** [abyss-samtobreak] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build/Misc' Makefile:440: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build' Makefile:359: recipe for target 'all' failed make: *** [all] Error 2 * ERROR: sci-biology/abyss-1.3.6::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/abyss-1.3.6::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/abyss-1.3.6::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:abyss-1.3.6:20150103-080713.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/abyss-1.3.6/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/abyss-1.3.6/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build' * S: '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6' * GNU info directory index is up-to-date. !!! existing preserved libs: >>> package: dev-libs/openobex-1.7.1 * - /usr/lib64/libopenobex.so.1 * - /usr/lib64/libopenobex.so.1.4.1 * used by /usr/bin/obex-data-server (app-mobilephone/obex-data-server-0.4.6) Use emerge @preserved-rebuild to rebuild packages using these libraries * IMPORTANT: config file '/etc/ppp/options' needs updating. * See the CONFIGURATION FILES section of the emerge * man page to learn how to update config files. This chroot image is located at a hardened amd64 host. Portage 2.2.15 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.8.4, glibc-2.20-r1, 3.17.7-hardened-r1 x86_64) ================================================================= System uname: Linux-3.17.7-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16166924 total, 409920 free KiB Swap: 16777212 total, 16755336 free Timestamp of tree: Sat, 03 Jan 2015 04:15:01 +0000 sh bash 4.3_p33 ld GNU ld (Gentoo 2.24 p1.4) 2.24 app-shells/bash: 4.3_p33 dev-lang/perl: 5.20.1-r4 dev-lang/python: 2.7.9-r1, 3.3.5-r1 dev-util/cmake: 3.0.2 dev-util/pkgconfig: 0.28-r2 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.13.6 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.11.6-r1, 1.14.1 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.8.4 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.4 sys-devel/make: 4.1-r1 sys-kernel/linux-headers: 3.18 (virtual/os-headers) sys-libs/glibc: 2.20-r1 Repositories: gentoo ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /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="-O2 -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --deep --jobs 1" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://gd.tuwien.ac.at/opsys/linux/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j1" 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" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.de.gentoo.org/gentoo-portage" USE="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mbox mmx modules multilib ncurses nls nptl openmp pam pax_kernel pcre readline session sse sse2 ssl tcpd unicode zlib" ABI_X86="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" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native -Wl,-O1 -Wl,--as-needed -o PathConsensus PathConsensus-PathConsensus.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build/MergePaths' Making all in Misc make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build/Misc' ghc --make -O2 -hidir ./ -odir ./ -o abyss-samtobreak /var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6/Misc/samtobreak.hs /var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6/Misc/samtobreak.hs:16:8: Could not find module ‘System.IO.MMap’ Use -v to see a list of the files searched for. Makefile:547: recipe for target 'abyss-samtobreak' failed make[2]: *** [abyss-samtobreak] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build/Misc' Makefile:449: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/abyss-1.3.6/work/abyss-1.3.6_build' Makefile:369: recipe for target 'all' failed make: *** [all] Error 2 * ERROR: sci-biology/abyss-1.3.6::gentoo failed (compile phase): * emake failed
This is automagic depend on GHC but it does not test for dev-haskell/mmap library availability. Added USE=misc-haskell to guard proper deps around it and tweak a ghc detection knob based on it. Pushed as: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a50e1769e82e28dedb16083ac9136f17f9af2297 Thank you!
I still get it with: Making all in Misc make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-1.3.6-r1/work/abyss-1.3.6_build/Misc' ghc --make -O2 -hidir ./ -odir ./ -o abyss-samtobreak /var/tmp/portage/sci-biology/abyss-1.3.6-r1/work/abyss-1.3.6/Misc/samtobreak.hs /var/tmp/portage/sci-biology/abyss-1.3.6-r1/work/abyss-1.3.6/Misc/samtobreak.hs:16:8: Could not find module `System.IO.MMap' Use -v to see a list of the files searched for. Makefile:547: recipe for target 'abyss-samtobreak' failed make[2]: *** [abyss-samtobreak] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-1.3.6-r1/work/abyss-1.3.6_build/Misc' # eselect ruby list Available Ruby profiles: [1] ruby20 (with Rubygems) * [2] ruby21 (with Rubygems) # # eselect ruby set 1 Successfully switched to profile: ruby20 # # emerge -pv eselect [ebuild U ] app-admin/eselect-1.4.5::gentoo [1.4.4::gentoo] USE="-doc -emacs -vim-syntax" 172 KiB # # emerge -uN eselect # eselect ruby set 1 # Still happens. # emerge -pv eselect-ruby [ebuild R ] app-eselect/eselect-ruby-20131227::gentoo 0 KiB # So I have no idea what I have outdated. Am on amd64 stable, true. # emerge --info WARNING: One or more repositories have missing repo_name entries: /var/lib/layman/profiles/repo_name NOTE: Each repo_name entry should be a plain text file containing a unique name for the repository on the first line. Portage 2.2.26 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.9.3, glibc-2.21-r2, 3.18.28-default x86_64) ================================================================= System uname: Linux-3.18.28-default-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.2 KiB Mem: 16409848 total, 963532 free KiB Swap: 15647296 total, 15318940 free Timestamp of repository gentoo: Sat, 02 Apr 2016 10:30:01 +0000 sh bash 4.2_p53 ld GNU ld (Gentoo 2.24 p1.4) 2.24 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.2_p53::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.9-r1::gentoo, 3.3.5-r1::gentoo, 3.4.3::gentoo dev-util/cmake: 2.8.12.2-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.13.11::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.4_p6-r1::gentoo, 1.5-r1::gentoo, 1.9.6-r3::gentoo, 1.10.3::gentoo, 1.11.6::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.15::gentoo sys-devel/binutils: 2.24-r3::gentoo sys-devel/gcc: 4.3.5::gentoo, 4.4.7::gentoo, 4.5.4::gentoo, 4.6.3::gentoo, 4.7.3-r1::gentoo, 4.8.5::gentoo, 4.9.3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 science location: /var/lib/layman/science masters: gentoo priority: 0 x-portage location: /usr/local/portage masters: gentoo priority: 1 x-layman location: /var/lib/layman masters: gentoo priority: 2 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions /var/bind /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/php/cli-php5.5/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="-O2 -pipe -march=native" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="rsync://ftp.fi.muni.cz/pub/linux/gentoo/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" 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="X accessibility alsa amd64 amr apache apache2 berkdb bzip2 cairo cgi cli cracklib crypt cups cxx dbus device-mapper dri encode ffmpeg flac fontconfig fortran gd gdbm geoip gnutls hal iconv id3tag innodb java jce jpeg jpg kde ladspa laptop mad maildir mmx mmxext modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin ogg opengl openmp openssl pam pcre perl php png policykit postfix procmail python qt3support qt4 readline sasl seccomp server session sndfile spf sse sse2 ssl suexec svg syslog tcpd threads tiff truetype unicode usb wavpack xattr xml xorg xvfb zlib" ABI_X86="64 32" 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="mmx mmxext sse sse2 sse3 sse4_1 ssse3" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en cs cz" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="vesa" 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: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
(In reply to Martin Mokrejš from comment #3) > I still get it with: > > Making all in Misc > make[2]: Entering directory > '/var/tmp/portage/sci-biology/abyss-1.3.6-r1/work/abyss-1.3.6_build/Misc' > ghc --make -O2 -hidir ./ -odir ./ -o abyss-samtobreak > /var/tmp/portage/sci-biology/abyss-1.3.6-r1/work/abyss-1.3.6/Misc/samtobreak. > hs > > /var/tmp/portage/sci-biology/abyss-1.3.6-r1/work/abyss-1.3.6/Misc/samtobreak. > hs:16:8: > Could not find module `System.IO.MMap' > Use -v to see a list of the files searched for. > Makefile:547: recipe for target 'abyss-samtobreak' failed > make[2]: *** [abyss-samtobreak] Error 1 > make[2]: Leaving directory > '/var/tmp/portage/sci-biology/abyss-1.3.6-r1/work/abyss-1.3.6_build/Misc' What does emerge --info sci-biology/abyss show for you? Is it a ::gentoo ebuild?
# emerge --info sci-biology/abyss WARNING: One or more repositories have missing repo_name entries: /var/lib/layman/profiles/repo_name NOTE: Each repo_name entry should be a plain text file containing a unique name for the repository on the first line. Portage 2.2.26 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.9.3, glibc-2.21-r2, 3.18.28-default x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.18.28-default-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.2 KiB Mem: 16409848 total, 975652 free KiB Swap: 15647296 total, 15318992 free Timestamp of repository gentoo: Sat, 02 Apr 2016 10:30:01 +0000 sh bash 4.2_p53 ld GNU ld (Gentoo 2.24 p1.4) 2.24 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.2_p53::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.9-r1::gentoo, 3.3.5-r1::gentoo, 3.4.3::gentoo dev-util/cmake: 2.8.12.2-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.13.11::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.4_p6-r1::gentoo, 1.5-r1::gentoo, 1.9.6-r3::gentoo, 1.10.3::gentoo, 1.11.6::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.15::gentoo sys-devel/binutils: 2.24-r3::gentoo sys-devel/gcc: 4.3.5::gentoo, 4.4.7::gentoo, 4.5.4::gentoo, 4.6.3::gentoo, 4.7.3-r1::gentoo, 4.8.5::gentoo, 4.9.3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 science location: /var/lib/layman/science masters: gentoo priority: 0 x-portage location: /usr/local/portage masters: gentoo priority: 1 x-layman location: /var/lib/layman masters: gentoo priority: 2 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/polkit-1/actions /var/bind /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/php/cli-php5.5/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="-O2 -pipe -march=native" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news nostrip parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="rsync://ftp.fi.muni.cz/pub/linux/gentoo/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" 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="X accessibility alsa amd64 amr apache apache2 berkdb bzip2 cairo cgi cli cracklib crypt cups cxx dbus device-mapper dri encode ffmpeg flac fontconfig fortran gd gdbm geoip gnutls hal iconv id3tag innodb java jce jpeg jpg kde ladspa laptop mad maildir mmx mmxext modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin ogg opengl openmp openssl pam pcre perl php png policykit postfix procmail python qt3support qt4 readline sasl seccomp server session sndfile spf sse sse2 ssl suexec svg syslog tcpd threads tiff truetype unicode usb wavpack xattr xml xorg xvfb zlib" ABI_X86="64 32" 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="mmx mmxext sse sse2 sse3 sse4_1 ssse3" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en cs cz" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="vesa" 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: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON # emerge -pv sci-biology/abyss [ebuild N ~] sci-biology/abyss-1.3.6-r1::science USE="mpi openmp" 0 KiB Grr. Would you mind fixing it as well? Thank you.
> # emerge -pv sci-biology/abyss > [ebuild N ~] sci-biology/abyss-1.3.6-r1::science USE="mpi openmp" 0 KiB > > Grr. Would you mind fixing it as well? Thank you. Sure, i'm not a part of science team though. Thus might take some time: https://github.com/gentoo-science/sci/pull/608
