Created attachment 331558 [details] build.log I can't reinstall apbs since I installed sci-libs/mkl-11.0.0.079 from the science overlay. I attach the complete build.log. Just in case, I also installed dev-lang/icc-13.0.1.117 and dev-lang/ifc-13.0.1.117 from the science overlay. This is the end of the build.log: ============ /bin/sh ../../libtool --tag=F77 --mode=link /usr/bin/mpif77 -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../.. -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -lnsl -lutil -lgfortran -lm -lpthread -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--as-needed -o driver driver.o readhb.o ardriv.o ../../src/aaa_lib/libapbs.la -larpack -L/usr/lib64 /var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/bin/libapbsmainroutines.la /var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/src/aaa_lib/libapbs.la -L/var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/contrib/lib -lmaloc -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../.. -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -lnsl -lutil -lgfortran -lm -lpthread -L/usr/lib -lmpi -lm -L/opt/intel/composerxe-2013.0.079/mkl/lib/intel64 -lmkl_rt -lpthread -lz libtool: link: /usr/bin/mpif77 -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,-O1 -Wl,--as-needed -o .libs/driver driver.o readhb.o ardriv.o -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../.. ../../src/aaa_lib/.libs/libapbs.so -L/opt/intel/composerxe-2013.0.079/mkl/lib/intel64 -L/var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/contrib/lib /usr/lib64/libarpack.so -L/opt/intel/composerxe-2013.0.079/mkl/lib/ia32 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core /var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/bin/.libs/libapbsmainroutines.so /var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/src/aaa_lib/.libs/libapbs.so /usr/lib64//libmaloc.so -lreadline /usr/lib64/libmpi_f77.so /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/libgfortran.so -L/usr/lib /usr/lib64/libmpi.so /usr/lib64/libopen-rte.so /usr/lib64/libopen-pal.so -ldl -lnsl -lutil -lm -lmkl_rt -lpthread -lz -pthread -Wl,-rpath -Wl,/usr/lib64/ ../../src/aaa_lib/.libs/libapbs.so: undefined reference to `GOMP_parallel_start' ../../src/aaa_lib/.libs/libapbs.so: undefined reference to `omp_get_thread_num' ../../src/aaa_lib/.libs/libapbs.so: undefined reference to `GOMP_parallel_end' ../../src/aaa_lib/.libs/libapbs.so: undefined reference to `omp_get_num_threads' collect2: ld returned 1 exit status make[2]: *** [driver] Error 1 make[2]: se sale del directorio `/var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/tools/arpack' make[1]: *** [all-recursive] Error 1 make[1]: se sale del directorio `/var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/tools' make: *** [all-recursive] Error 1
Can you also provide the output of `emerge --info =sci-chemistry/apbs-1.3-r3`?
I will test that.
which blas and lapack did you eselect?
(In reply to comment #1) > Can you also provide the output of `emerge --info > =sci-chemistry/apbs-1.3-r3`? Sure: Portage 2.1.11.31 (default/linux/amd64/10.0/desktop/kde, gcc-4.5.4, glibc-2.15-r3, 3.5.7-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.5.7-gentoo-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q8300_@_2.50GHz-with-gentoo-2.1 Timestamp of tree: Mon, 03 Dec 2012 07:30:01 +0000 ld GNU ld (GNU Binutils) 2.22 app-shells/bash: 4.2_p37 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.3-r2, 3.2.3 dev-util/cmake: 2.8.9 dev-util/pkgconfig: 0.27.1 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.11.6 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.11.6 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.5.4 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.6 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: science gentoo local ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -mtune=core2 -O2 -pipe -msse4.1" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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=core2 -mtune=core2 -O2 -pipe -msse4.1" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps y" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://gentoo.mirror.dkm.cz/pub/gentoo/" LANG="es_ES.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="es_ES es en_US en" MAKEOPTS="-j5" PKGDIR="/home/ramiro/usr/local/portage/pkgdir-backup/" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --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="/var/lib/layman/science /usr/portage /usr/portage/local" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X X509 a52 aac aalib accessibility acl acpi additions adns alsa amd64 apache2 apbs apm apng archive arpack audiofile auth authfile autoipd autoreplace autotrace bash-completion bcmath bdf berkdb binary-drivers binfilter blas branding bzip2 cairo caps cdda cddb cdparanoia cdr cdrom chm chroot clamav cleartype cli compat consolekit contactnotes context cracklib crypt css ctype cups curl curlwrappers custom-optimization cxx dbus declarative designer-plugin desktopglobe detex dga dia directfb djvu dri dts dvd dvdr dvi dvipdfm emboss emf emovix enca encode exif expoblending extensions extra fam fastcgi fat fbcon ffmpeg fftw firefox firefox3 flac flatfile fontconfig foomaticdb fortran fpx ftp fuse gallium gd gdbm geoip geolocation gif gimp git gmp google gphoto2 gpm gps gpssync grammar graphics graphviz grub gsl gtk gzip hddtemp hdri hfs history hpcups hpijs hpn humanities iconv icu id3tag idn ieee1394 imagemagick imap imlib inifile inkjar ipv6 jack jadetex java java6 javascript jbig jce jfs jpeg jpeg2k justify kde kipi ladspa lame lapack latex lcms ldap lensfun libcaca libnotify libssh2 libwww live lm_sensors logrotate loop-aes lqr lua lzo m17n-lib mad maildir mailwrapper math matroska mbox mcve md5sum mdb mediawiki memlimit milter mime mjpeg mkl mmap mmx mmxext mng modplug modules mono motif mozilla mp3 mp4 mpeg mpi mplayer msn mudflap multilib multiuser musepack music musicbrainz nas ncurses neXt net netboot network network-cron networking networkmanager new-login nis nls npp nptl nsplugin ntfs ntfsprogs numpy nvidia ofx ogg omega openal openbabel openexr opengl openmp openssl opensslcrypt osc ots pam pango panorama parse-clocks pcntl pcre pdf phonon plasma plotutils plugins png policykit portaudio posix postproc povray ppds profile pstricks publishers qt3support qt4 quicktime rar raster raw rdesktop readline redeyes reiserfs resolvconf rss rtc rtf rtsp ruby samba sasl scanner science sdk sdl sdl-image semantic-desktop sensord session shout simplexml skey skins slang slp snmp soap sockets socks5 solver source sox speex spell sse sse2 sse3 sse4 sse41 sse4_1 ssl ssse3 startup-notification subtitles subversion svg swat syslog sysvipc szip t1lib taglib tcl tcpd tex4ht tga theora thesaurus threads thumbnail thunderbird tidy tiff tk truetype twolame udev udisks unicode upower usb userlocales v4l vcd vcdx vlm vmd vnc vorbis wavpack wddx webdav winbind winpopup wmf wxwidgets x264 xanim xattr xcb xcomposite xetex xface xforms xfs xft xindy xine xinerama xls xml xmlreader xmlrpc xmlwriter xorgmodule xplanet xpm xscreensaver xsl xv xvid xvmc zip zlib zoran" ALSA_CARDS="hda-intel" 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 auth_digest authn_anon authn_dbd 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 dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" FOO2ZJS_DEVICES="hp1000" 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 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="es_ES es en_US en" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" SANE_BACKENDS="epson2 hp samsung" USERLAND="GNU" VIDEO_CARDS="nvidia" 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
(In reply to comment #3) > which blas and lapack did you eselect? blas: [7] mkl64-dynamic * lapack: [7] mkl64-dynamic * I will be happy to change them to safer/more appropriate ones if required.
please try mkl64-intel or mkl64-intel-openmp
(In reply to comment #6) > please try mkl64-intel or mkl64-intel-openmp * mkl64-intel: same error as before * mkl64-intel-openmp: different error: ================= libtool: link: /usr/bin/mpif77 -O2 -pipe -march=core2 -mtune=core2 -O2 -pipe -msse4.1 -fopenmp -Wl,-O1 -Wl,--as-needed -O2 -pipe -Wl,-O1 -Wl,--as-needed -o .libs/apbs main.o -Wl,--start-group -Wl,--end-group -openmp -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/../../.. /var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/bin/.libs/libapbsmainroutines.so -L/opt/intel/composerxe-2013.0.079/mkl/lib/intel64 -L/var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/contrib/lib -L/usr/lib .libs/libapbsmainroutines.so /var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/src/aaa_lib/.libs/libapbs.so /usr/lib64/libmpi_f77.so /usr/lib64/libmpi.so /usr/lib64/libopen-rte.so /usr/lib64/libopen-pal.so -ldl -lnsl -lutil /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.4/libgfortran.so -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread /usr/lib64//libmaloc.so -lreadline -lm -lz -pthread -Wl,-rpath -Wl,/usr/lib64/ /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_single' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_ordered' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_barrier' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_critical' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx8_add' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float4_add' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `ompc_set_nested' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_4' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_flush' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_single' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_float8_add' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_master' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_fini' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_master' /opt/intel/composerxe-2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_cmplx4_add' collect2: ld returned 1 exit status make[2]: *** [apbs] Error 1 make[2]: se sale del directorio `/var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/bin' make[1]: *** [all] Error 2 make[1]: se sale del directorio `/var/tmp/portage/sci-chemistry/apbs-1.3-r3/work/apbs-1.3-source/bin' make: *** [all-recursive] Error 1
The problem is gone after rebuilding these packages (others, like python and numpy, had been recompiled with icc way in advance but apbs kept failing): emerge -1 dev-libs/glib dev-libs/libgcrypt dev-libs/libgpg-error dev-libs/libxml2 dev-libs/lzo media-libs/freetype media-libs/giflib media-libs/libpng sci-libs/arpack sys-libs/readline dev-libs/maloc sci-chemistry/apbs Some of the packages are on the above command because I got them in my package.icc as per the icc guide in Gentoo wiki: --------------------- # From the icc guide in Gentoo Wiki # http://en.gentoo-wiki.com/wiki/Intel_C%2B%2B_Compiler app-arch/bzip2 app-arch/cpio app-arch/gzip app-arch/tar app-arch/unzip dev-db/sqlite dev-lang/python dev-libs/glib dev-libs/libgcrypt dev-libs/libgpg-error dev-libs/libxml2 dev-libs/lzo media-gfx/gimp media-libs/faac media-libs/freetype media-libs/giflib media-libs/libogg media-libs/libpng media-libs/libtheora media-libs/libvorbis media-libs/speex media-libs/x264-svn media-libs/xvid media-sound/lame net-irc/xchat sys-fs/cryptsetup sys-power/powertop x11-libs/gtk+ # My packages sci-chemistry/autodock_vina sci-libs/mkl sci-libs/clapack sci-libs/arpack sci-chemistry/scala sci-chemistry/pymol dev-python/numpy dev-python/pmw media-libs/opencv
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3831172264494f42d621e760593f4d066900d922 commit 3831172264494f42d621e760593f4d066900d922 Author: Aaron Bauman <bman@gentoo.org> AuthorDate: 2020-07-28 18:45:29 +0000 Commit: Aaron Bauman <bman@gentoo.org> CommitDate: 2020-07-28 18:45:29 +0000 */*: Drop more Py2 last-rited pkgs Bug: https://bugs.gentoo.org/715966 Closes: https://bugs.gentoo.org/714628 Closes: https://bugs.gentoo.org/606680 Closes: https://bugs.gentoo.org/686238 Closes: https://bugs.gentoo.org/710214 Closes: https://bugs.gentoo.org/710028 Closes: https://bugs.gentoo.org/710032 Closes: https://bugs.gentoo.org/656934 Closes: https://bugs.gentoo.org/592718 Closes: https://bugs.gentoo.org/446122 Closes: https://bugs.gentoo.org/547210 Closes: https://bugs.gentoo.org/359785 Closes: https://bugs.gentoo.org/571396 Closes: https://bugs.gentoo.org/600754 Closes: https://bugs.gentoo.org/677830 Closes: https://bugs.gentoo.org/710716 Closes: https://bugs.gentoo.org/651940 Closes: https://bugs.gentoo.org/695132 Closes: https://bugs.gentoo.org/708978 Closes: https://bugs.gentoo.org/710058 Signed-off-by: Aaron Bauman <bman@gentoo.org> app-backup/holland-backup-example/Manifest | 1 - .../holland-backup-example-1.0.10.ebuild | 39 ----- app-backup/holland-backup-example/metadata.xml | 5 - app-backup/holland-backup-pgdump/Manifest | 1 - .../holland-backup-pgdump-1.0.10.ebuild | 38 ----- app-backup/holland-backup-pgdump/metadata.xml | 5 - app-backup/holland-backup-random/Manifest | 1 - .../holland-backup-random-1.0.10.ebuild | 39 ----- app-backup/holland-backup-random/metadata.xml | 5 - app-backup/holland-backup-sqlite/Manifest | 1 - .../holland-backup-sqlite-1.0.10.ebuild | 39 ----- app-backup/holland-backup-sqlite/metadata.xml | 5 - app-backup/holland-lib-common/Manifest | 1 - .../holland-lib-common-1.0.10.ebuild | 25 ---- app-backup/holland-lib-common/metadata.xml | 5 - app-backup/holland-lib-lvm/Manifest | 1 - .../holland-lib-lvm/holland-lib-lvm-1.0.10.ebuild | 25 ---- app-backup/holland-lib-lvm/metadata.xml | 5 - app-backup/holland/Manifest | 1 - app-backup/holland/holland-1.0.10.ebuild | 54 ------- app-backup/holland/metadata.xml | 5 - app-cdr/burn-cd/Manifest | 2 - app-cdr/burn-cd/burn-cd-1.8.0-r1.ebuild | 31 ---- app-cdr/burn-cd/burn-cd-1.8.1.ebuild | 27 ---- app-cdr/burn-cd/metadata.xml | 16 --- app-dicts/opendict/Manifest | 1 - app-dicts/opendict/metadata.xml | 11 -- app-dicts/opendict/opendict-0.6.7-r1.ebuild | 91 ------------ app-editors/editra/Manifest | 1 - app-editors/editra/editra-0.7.20-r2.ebuild | 54 ------- app-editors/editra/files/editra-0.7.20-wx30.patch | 44 ------ app-editors/editra/metadata.xml | 8 -- app-editors/leo/Manifest | 1 - app-editors/leo/leo-5.6.ebuild | 36 ----- app-editors/leo/metadata.xml | 9 -- app-emulation/playonlinux/Manifest | 2 - .../files/playonlinux-4.2.4-binary-plugin.patch | 17 --- .../files/playonlinux-4.2.4-pol-bash.patch | 35 ----- .../playonlinux-4.2.6-stop-update-warning.patch | 17 --- app-emulation/playonlinux/files/playonlinux-pkg.1 | 33 ----- app-emulation/playonlinux/files/playonlinux.1 | 33 ----- app-emulation/playonlinux/metadata.xml | 15 -- .../playonlinux/playonlinux-4.2.12.ebuild | 118 --------------- .../playonlinux/playonlinux-4.3.4-r1.ebuild | 108 -------------- app-office/taskcoach/Manifest | 1 - .../files/taskcoach-1.4.3-version-check.patch | 25 ---- app-office/taskcoach/metadata.xml | 21 --- app-office/taskcoach/taskcoach-1.4.6.ebuild | 41 ------ app-text/bibus/Manifest | 2 - app-text/bibus/bibus-1.5.2-r3.ebuild | 86 ----------- app-text/bibus/files/bibus-1.5.2-bibus.cfg.patch | 31 ---- app-text/bibus/files/bibus-1.5.2-install.patch | 110 -------------- app-text/bibus/files/bibus-1.5.2-wx30.patch | 158 --------------------- app-text/bibus/metadata.xml | 11 -- dev-db/SchemaSync/Manifest | 3 - dev-db/SchemaSync/SchemaSync-0.9.2-r1.ebuild | 24 ---- dev-db/SchemaSync/SchemaSync-0.9.4.ebuild | 23 --- dev-db/SchemaSync/SchemaSync-0.9.5.ebuild | 23 --- dev-db/SchemaSync/metadata.xml | 12 -- dev-python/squaremap/Manifest | 1 - dev-python/squaremap/metadata.xml | 15 -- dev-python/squaremap/squaremap-1.0.4.ebuild | 26 ---- dev-util/wxglade/Manifest | 1 - .../wxglade/files/wxglade-0.6.3-wxversion.patch | 12 -- dev-util/wxglade/metadata.xml | 11 -- dev-util/wxglade/wxglade-0.8.2-r1.ebuild | 55 ------- media-gfx/fontypython/Manifest | 1 - .../0001-Do-not-crash-on-empty-pogs-list.patch | 21 --- ...nused-code-which-causes-crash-with-wx-3.0.patch | 134 ----------------- ...python-3.0-which-enforces-assertions-on-L.patch | 28 ---- .../fontypython/files/fontypython-pillow.patch | 41 ------ media-gfx/fontypython/fontypython-0.4.4-r3.ebuild | 38 ----- media-gfx/fontypython/metadata.xml | 8 -- media-gfx/fr0st/Manifest | 1 - media-gfx/fr0st/files/fr0st-1.4-colour.patch | 9 -- media-gfx/fr0st/fr0st-1.4-r2.ebuild | 57 -------- media-gfx/fr0st/metadata.xml | 8 -- profiles/package.mask | 38 ----- sci-chemistry/apbs/Manifest | 1 - sci-chemistry/apbs/apbs-1.4.1-r2.ebuild | 129 ----------------- sci-chemistry/apbs/files/apbs-1.4.1-manip.patch | 50 ------- sci-chemistry/apbs/files/apbs-1.4.1-multilib.patch | 92 ------------ sci-chemistry/apbs/files/apbs-1.4.1-python.patch | 122 ---------------- sci-chemistry/apbs/metadata.xml | 25 ---- sci-chemistry/eden/Manifest | 1 - sci-chemistry/eden/eden-5.3-r2.ebuild | 88 ------------ sci-chemistry/eden/files/5.3-makefile-fixes.patch | 60 -------- .../eden/files/eden-5.3-format-security.patch | 96 ------------- sci-chemistry/eden/files/eden-5.3-impl-dec.patch | 28 ---- sci-chemistry/eden/files/makefile-fixes.patch | 25 ---- sci-chemistry/eden/metadata.xml | 12 -- sci-chemistry/p3d/Manifest | 1 - sci-chemistry/p3d/metadata.xml | 21 --- sci-chemistry/p3d/p3d-0.4.3-r1.ebuild | 29 ---- sci-chemistry/p3d/p3d-9999.ebuild | 27 ---- sci-chemistry/pdb-tools/Manifest | 1 - sci-chemistry/pdb-tools/metadata.xml | 12 -- sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild | 79 ----------- sci-chemistry/pdb-tools/pdb-tools-0.2.1-r2.ebuild | 83 ----------- sci-chemistry/pdb2pqr/Manifest | 1 - sci-chemistry/pdb2pqr/files/pdb2pka | 13 -- sci-chemistry/pdb2pqr/files/pdb2pqr | 13 -- .../pdb2pqr/files/pdb2pqr-1.9.0-flags.patch | 45 ------ .../pdb2pqr/files/pdb2pqr-1.9.0-install-py.patch | 15 -- sci-chemistry/pdb2pqr/metadata.xml | 15 -- sci-chemistry/pdb2pqr/pdb2pqr-1.9.0-r3.ebuild | 114 --------------- sci-chemistry/prodecomp/Manifest | 1 - sci-chemistry/prodecomp/metadata.xml | 18 --- sci-chemistry/prodecomp/prodecomp-3.0-r3.ebuild | 53 ------- sci-chemistry/pymol-plugins-caver/Manifest | 1 - sci-chemistry/pymol-plugins-caver/metadata.xml | 8 -- .../pymol-plugins-caver-2.1.2.ebuild | 56 -------- sci-chemistry/pymol-plugins-dssp/Manifest | 1 - sci-chemistry/pymol-plugins-dssp/metadata.xml | 8 -- .../pymol-plugins-dssp-110430-r1.ebuild | 39 ----- sci-chemistry/pymol-plugins-promol/Manifest | 1 - sci-chemistry/pymol-plugins-promol/metadata.xml | 8 -- .../pymol-plugins-promol-3.0.2-r1.ebuild | 60 -------- sci-chemistry/sparky/Manifest | 1 - sci-chemistry/sparky/files/3.115-fix-c++14.patch | 32 ----- sci-chemistry/sparky/files/3.115-ldflags.patch | 61 -------- sci-chemistry/sparky/files/3.115-makefile.patch | 17 --- sci-chemistry/sparky/files/3.115-paths.patch | 13 -- sci-chemistry/sparky/files/3.115-wrapper-r1.patch | 41 ------ sci-chemistry/sparky/metadata.xml | 8 -- sci-chemistry/sparky/sparky-3.115-r2.ebuild | 117 --------------- www-apps/viewvc/Manifest | 1 - www-apps/viewvc/metadata.xml | 13 -- www-apps/viewvc/viewvc-1.1.26-r1.ebuild | 115 --------------- 129 files changed, 3958 deletions(-)
