For some reason, portage does not want to accept my installed virtual/jre-1.6.0 to satisfy >=virtual/jre-1.5.0 requirement of dev-lang/R. If I change the dependeny to >=virtual/jre-1.6.0, it seems to work fine. # emerge -pt1v R These are the packages that would be merged, in reverse order: Calculating dependencies ... done! [ebuild R ] dev-lang/R-2.10.1 USE="X bash-completion cairo java jpeg nls perl png readline -doc -lapack -minimal -threads -tk" 0 kB [ebuild NS ] virtual/jdk-1.5.0 [1.6.0] 0 kB [ebuild N F ] dev-java/ibm-jdk-bin-1.5.0.12_p1 USE="X javacomm odbc (-alsa) -doc -examples (-nsplugin)" 66,482 kB Total: 3 packages (1 new, 1 in new slot, 1 reinstall), Size of downloads: 66,482 kB Fetch Restriction: 1 package (1 unsatisfied) # USE=-java emerge -pt1v R These are the packages that would be merged, in reverse order: Calculating dependencies ... done! [ebuild R ] dev-lang/R-2.10.1 USE="X bash-completion cairo jpeg nls perl png readline -doc -java* -lapack -minimal -threads -tk" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB # emerge -pv '>=virtual/jre-1.5' These are the packages that would be merged, in order: Calculating dependencies ... done! [ebuild R ] virtual/jre-1.6.0 0 kB [?=>0] Total: 1 package (1 reinstall), Size of downloads: 0 kB Portage tree and overlays: [0] /usr/portage [?] indicates that the source repository could not be determined # emerge --info Portage 2.2.0_alpha15 (default/linux/amd64/10.0, gcc-4.4.4, glibc-2.11.2-r3, 2.6.34-hardened-r6 x86_64) ================================================================= System uname: Linux-2.6.34-hardened-r6-x86_64-AMD_Athlon-tm-_64_Processor_2800+-with-gentoo-2.0.1 Timestamp of tree: Sat, 15 Jan 2011 09:45:01 +0000 app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.6.6-r1, 3.1.2-r4 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13::<unknown repository>, 2.65-r1 sys-devel/automake: 1.9.6-r2::<unknown repository>, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.4.4-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.10 sys-devel/make: 3.81-r2 virtual/os-headers: 2.6.30-r1 (sys-kernel/linux-headers) Repositories: gentoo anarchy hardened-dev eradicator ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -fomit-frame-pointer -march=k8" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config" 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-php5.3/ext-active/ /etc/php/cgi-php5.3/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="-O2 -pipe -O2 -pipe -fomit-frame-pointer -march=k8" DISTDIR="/var/tmp/gentoo/distfiles" FEATURES="assume-digests binpkg-logs candy collision-protect distlocks fixlafiles fixpackages metadata-transfer news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS="http://gentoo.osuosl.org/ http://gentoo.mirrors.pair.com/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en en_US" MAKEOPTS="-j1" PKGDIR="/var/tmp/gentoo/packages-amd64" 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/anarchy /var/lib/layman/hardened-development /usr/local/portage" SYNC="rsync://rsync15.us.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 3ds S3TC X X509 Xaw3d a52 aac aalib acl acpi activefilter adplug aim alltargets alsa amd amd64 amr ao apache2 artworkextra atlas audiofile avahi avantgo bash-completion bcmath berkdb bidi browserplugin bzip2 bzlib c++ cairo calendar caps cdda cddb cdio cdparanoia cdr cgi chroot clamav clamd clamdtop clanJavaScript clanVoice clearpasswd cli client clisp consolekit coverage cracklib crypt cscope css cups curl curlwrappers cvs cvsgraph cxx dbase dbcp dbm dbus dbx dedicated device-mapper dga dio divx4linux dlloader dmx dnd dri dts dv dvd dvdr dvdread edl eds emacs emacs-w3 enca encode enscript erandom esd ethereal evms2 evo exif exiv2 expat ext-png ext-zlib extensions f77 faac faad fam fame fat fax fbcon fbdev ffmpeg fftw filter firefox flac flash flatfile fltk fluidsynth font-server fontconfig foomaticdb fortran fpx freetts freetype fs fts3 gb gcj gcl gd gd-external gdbm gdu geoip gif gimp gimpprint git glade glep glib glibc-omitfp glitz glut gmp gmtfull gmthigh gmtsuppl gmttria gnome gnomedb gnuplot gnutls gocr gpm gps graphviz gs gstreamer gtk gtkhtml hal hash hbci hdri highlight howl howl-compat hyperestraier iconv icq idea idl idn ieee1394 image imagemagick imap imlib imlib2 inifile innodb ipalias iproute2 ipsec ipv6 ithreads jabber jack java javacomm javamail javascript jbig jikes joystick jpeg jpeg2k junit justify kde kdrive ladcca latex lcms ldap libcaca libclamav libdsk libedit libg++ libgda libsamplerate libwww lids live llvm llvm-gcc lm_sensors lmtp log4j logitech-mouse ltsp lua lucid lzo mad maildir makecheck matroska mbrola mcal md5sum mdnsresponder-compat mercurial mhash mikmod mime ming mixer mjpeg mmx mmxext mng mod_python modules mozcalendar mozctl mozdevelop mozilla mozp3p mozsvg mozxmlterm mp2 mp3 mpeg mpeg4 mplayer mpm-prefork msession msn mtp mudflap mule multilib multislot musepack music mysql mysqli mythtv nas native ncurses neXt network nis nls nptl nptlonly nsplugin nviz oav objc objc++ objc-gc ocaml ocrad odbc offensive ofx ogg oggvorbis oldworld openal opendoc openexr opengl openmp openssl opensslcrypt opera oscar oss pam pango parse-clocks pcap pch pcntl pcre pda pdf perl php physfs pic pie plotutils png pnm pnp policykit portaudio povray ppds pppd prelude procmail pulseaudio python q32 qhull qt-webkit qt3support qt4 quicktime rar readline recode regexp rplay rtc samba sasl savedconfig sdk sdl sdl-image semantic-desktop server session sharedmem sid silc slp sms sndfile soap socks5 soup sox speex spell sql sqlite sqlite3 src srt sse sse2 ssl startup-notification static-analyzer subversion suexec svg sysfs system-cxx-headers sysvipc t1lib tcltk tcpd tesseract tetex tex tga theora thunar thunderbird tidy tiff timidity transcode transparent-proxy truetype trusted tta type1 ucs2 udev udis86 unicode urandom usb user-homedirs userlocales v4l v4l2 vcd vda vhosts videos vim-with-x virus-scan visualization vlm vnc vorbis wav wavpack wddx webkit wma wmf wsconvert wxwin wxwindows x264 xanim xattr xchattext xcomposite xemacs xface xforms xfs xine xinerama xml xml2 xmlreader xmlrpc xmlwriter xorg xosd xpm xsl xulrunner xv xvid xvmc yahoo zeo zeroconf zip zlib" ALSA_CARDS="via82xx" 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 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" 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="wacom joystick keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en en_US" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia nv nouveau" 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, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
(In reply to comment #0) > # emerge -pv '>=virtual/jre-1.5' > > These are the packages that would be merged, in order: > > Calculating dependencies ... done! > [ebuild R ] virtual/jre-1.6.0 0 kB [?=>0] I suspect that the problem will disappear if you reinstall this package. Can you create a tarball of /var/db/pkg/virtual/jre-1.6.0/ and attach it please?
(In reply to comment #0) > # emerge -pt1v R Also, can you check if adding the -u option makes it reinstall virtual/jre-1.6.0 automatically, instead of pulling in virtual/jre-1.5.0?
Created attachment 260209 [details] virts.tar.bz2 tar cjf /tmp/virts.tar.bz2 virtual/jre-* virtual/jdk-*
(In reply to comment #2) > (In reply to comment #0) > > # emerge -pt1v R > > Also, can you check if adding the -u option makes it reinstall > virtual/jre-1.6.0 automatically, instead of pulling in virtual/jre-1.5.0? > # emerge -pt1vu R These are the packages that would be merged, in reverse order: Calculating dependencies ... done! Total: 0 packages, Size of downloads: 0 kB # emerge -pt1v R These are the packages that would be merged, in reverse order: Calculating dependencies ... done! [ebuild R ] dev-lang/R-2.10.1 USE="X bash-completion cairo java jpeg nls perl png readline -doc -lapack -minimal -threads -tk" 0 kB [ebuild NS ] virtual/jdk-1.5.0 [1.6.0] 0 kB [ebuild N F ] dev-java/ibm-jdk-bin-1.5.0.12_p1 USE="X javacomm odbc (-alsa) -doc -examples (-nsplugin)" 66,482 kB Total: 3 packages (1 new, 1 in new slot, 1 reinstall), Size of downloads: 66,482 kB Fetch Restriction: 1 package (1 unsatisfied)
(In reply to comment #1) > (In reply to comment #0) > > # emerge -pv '>=virtual/jre-1.5' > > > > These are the packages that would be merged, in order: > > > > Calculating dependencies ... done! > > [ebuild R ] virtual/jre-1.6.0 0 kB [?=>0] > > I suspect that the problem will disappear if you reinstall this package. Your suspicions seem to be validated. After re-emerging that virtual, I have: # emerge -pt1v R These are the packages that would be merged, in reverse order: Calculating dependencies ... done! [ebuild R ] dev-lang/R-2.10.1 USE="X bash-completion cairo java jpeg nls perl png readline -doc -lapack -minimal -threads -tk" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB
This is fixed in git: http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=2553847b6b7795719ee7b4439f34182dcd66fcae It's a regression from the fix for bug 350285.
This is fixed in 2.1.9.34 and 2.2.0_alpha18.
