'perl-cleaner --reallyall' fails with: ... [ebuild R ] dev-perl/Bio-Das-1.17 0 kB [0] [ebuild R ] dev-perl/Bio-ASN1-EntrezGene-1.091 USE="-test" 0 kB [0] [ebuild U *] sci-biology/bioperl-9999-r1 [1.6.9] USE="db graphviz network run -minimal (-sqlite%*)" 0 kB [0] [ebuild U *] sci-biology/bioperl-db-9999-r1 [1.6.9] USE="(-test%)" 0 kB [0] [ebuild U *] sci-biology/bioperl-network-9999-r1 [1.6.9] USE="-test" 0 kB [0] [ebuild U *] sci-biology/bioperl-run-9999-r1 [1.6.9] USE="-minimal -test" 0 kB [0] [ebuild R ] dev-perl/Bio-SamTools-1.29 0 kB [0=>4] [ebuild R ] sci-biology/GBrowse-2.39 USE="mysql postgres sqlite -minimal -vhosts" 0 kB [0] Total: 397 packages (5 upgrades, 2 new, 390 reinstalls), Size of downloads: 0 kB Portage tree and overlays: [0] /usr/portage [1] /var/lib/cpan [2] /usr/local/portage [3] /var/lib/layman/sunrise [4] /var/lib/layman/science The following keyword changes are necessary to proceed: #required by sci-biology/bioperl-9999-r1[run], required by sci-biology/bioperl-network-9999-r1, required by sci-biology/bioperl-network:0 (argument) >=sci-biology/bioperl-run-9999-r1 ** #required by sci-biology/bioperl-9999-r1[db], required by sci-biology/bioperl-network-9999-r1, required by sci-biology/bioperl-network:0 (argument) >=sci-biology/bioperl-db-9999-r1 ** #required by sci-biology/bioperl-network-9999-r1, required by sci-biology/bioperl-network:0 (argument) >=sci-biology/bioperl-9999-r1 ** #required by sci-biology/bioperl-9999-r1[network], required by sci-biology/bioperl-run-9999-r1, required by sci-biology/bioperl-run:0 (argument) >=sci-biology/bioperl-network-9999-r1 ** What should I do? I tried to set sci-biology/bioperl ~* * sci-biology/bioperl-run ~* * sci-biology/bioperl-network ~* * sci-biology/bioperl-db ~* * in /etc/portage/packages.keywords, but this does not changed anything. Reproducible: Always root@impala:/root(11)# emerge --info Portage 2.1.10.11 (default/linux/amd64/10.0, gcc-4.5.3, glibc-2.13-r4, 3.0.0-gentoo x86_64) ================================================================= System uname: Linux-3.0.0-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.0.3 Timestamp of tree: Mon, 15 Aug 2011 06:00:01 +0000 app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r2, 3.2-r2 dev-util/cmake: 2.8.5-r2 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.0.3 sys-apps/openrc: 0.8.3-r1 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1-r1 sys-devel/binutils: 2.21.1 sys-devel/gcc: 4.5.3-r1 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 2.6.39 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo x11 sunrise lordvan java-overlay bicatali science x-portage x-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=amdfam10 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/ext-active/ /etc/php/cli-php5.3/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=amdfam10 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LC_ALL="C" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/sunrise /var/lib/layman/lordvan /var/lib/layman/java-overlay /var/lib/layman/bicatali /var/lib/layman/science /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac abiword accessibility acl acpi admin afs alsa amd64 amrr ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4a ssl subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" 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 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 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="braindump flow karbon kexi kpresenter krita tables words" 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 ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nouveau 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
(In reply to comment #0) You can copy and paste the following to package.(accept_)keywords: > #required by sci-biology/bioperl-9999-r1[run], required by > sci-biology/bioperl-network-9999-r1, required by sci-biology/bioperl-network:0 > (argument) > >=sci-biology/bioperl-run-9999-r1 ** > #required by sci-biology/bioperl-9999-r1[db], required by > sci-biology/bioperl-network-9999-r1, required by sci-biology/bioperl-network:0 > (argument) > >=sci-biology/bioperl-db-9999-r1 ** > #required by sci-biology/bioperl-network-9999-r1, required by > sci-biology/bioperl-network:0 (argument) > >=sci-biology/bioperl-9999-r1 ** > #required by sci-biology/bioperl-9999-r1[network], required by > sci-biology/bioperl-run-9999-r1, required by sci-biology/bioperl-run:0 > (argument) > >=sci-biology/bioperl-network-9999-r1 ** > What should I do? I tried to set > > sci-biology/bioperl ~* * > sci-biology/bioperl-run ~* * > sci-biology/bioperl-network ~* * > sci-biology/bioperl-db ~* * You need the double asterisk (see man portage): | ** package is always visible (KEYWORDS are ignored completely) But this is not bug in perl-cleaner
Thanks Torsten for the hint with the double asterisk. But I do not yet understand why 'perlcleaner --reallyall' want to install this strange (9999-r1) version of bioperl, bioperl-db, bioperl-network and bioperl-run, while 'emerge -pvD bioperl' installs bioperl-1.6.9. What is changed in the 9999-r1 version against the 1.6.9 version. The most current version on the bioperl website is also 1.6.9. What is recommended to do? Set theese double asterisks in /etc/portage/packages.keywords or wait with 'perlcleaner --reallyall' until the next major perl-update or until the next regular bioperl version? Regards Juergen
It tries to install Bio-SamTools from the science overlay: dev-perl/Bio-SamTools-1.29 0 kB [0=>4] This ebuild[1] depends on >=sci-biology/bioperl-1.6.901. The only availble version seems to be ~9999. [1] http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=blob;f=dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild;h=1b985ff5b01bc0d9c661d5cb545d0f7d09f4767d;hb=HEAD
I installed sci-biology/GBrowse-2.39. It depends on >=dev-perl/Bio-SamTools-1.20. I have dev-perl/Bio-SamTools at two places (/usr/portage/dev-perl/Bio-SamTools and /var/lib/layman/science/dev-perl/Bio-SamTools). At both places is only one ebuild (Bio-SamTools-1.29.ebuild): root@impala:/root(59)# ll /usr/portage/dev-perl/Bio-SamTools/Bio* /var/lib/layman/science/dev-perl/Bio-SamTools/Bio* -rw-r--r-- 1 root root 895 Jul 20 02:43 /usr/portage/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild -rw-r--r-- 1 root root 1096 Aug 7 13:38 /var/lib/layman/science/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild /usr/portage/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild depends on sci-biology/bioperl. /var/lib/layman/science/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild depends on >=sci-biology/bioperl-1.6.901. Is there the possibility to mask only /var/lib/layman/science/dev-perl/Bio-SamTools/Bio-SamTools-1.29.ebuild? Or is it better to deinstall GBrowse to solve the version conflict? Regards Juergen
dev-perl/Bio-SamTools was removed from the overlay (bug #379539): http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=88b992c6 perl-cleaner should work again as expected. Remember to remove the unwanted entries from /etc/portage/package.keywords. Thanks
Thanks Torsten, the remaining problem is that 'perl-cleaner --reallyall' hangs now to reemerge PDL, but this is another issue. Regards Juergen
