Even 'emerge -vuND --backtrack=30 world' fails with: root@wildcat:/root(11)# emerge -vuND --backtrack=30 world ... [ebuild U ] sci-libs/netcdf-4.3.0::gentoo [4.1.3::x-portage] USE="dap* doc examples%* hdf%* hdf5 mpi%* szip%* tools%* -static-libs {-test%} (-cxx%*) (-fortran%*)" 0 kB ... !!! Multiple package instances within a single package slot have been pulled !!! into the dependency graph, resulting in a slot conflict: sci-libs/netcdf:0 (sci-libs/netcdf-4.3.0::gentoo, ebuild scheduled for merge) pulled in by (no parents that aren't satisfied by other packages in this slot) (sci-libs/netcdf-4.1.3::x-portage, installed) pulled in by ~sci-libs/netcdf-4.1.3[cxx,hdf5] required by (sci-visualization/paraview-4.0.1-r1::gentoo, installed) It may be possible to solve this problem by using package.mask to prevent one of those packages from being selected. However, it is also ... root@wildcat:/root(12)# I think, that I can solve this issue by masking >sci-libs/netcdf-4.1.3. But I have the feeling, that in the last time there is a cumulation of these slot conflicts, which are not managed by emerge. In the past emerge was complaining about this issue, but did not stop to emerge the rest of the world.
Can we please see the complete output of that? Please add --tree --unordered-display that clarifies what is pulling in what. Can you also comment with the output of `emerge --info`? Please note that one of the slot conflict packages is from your local overlay; so, you might be able to resolve this in that place (perhaps by removing it).
I reach this computer (wildcat) probably again at monday. But here I have a similar problem on the next system: root@condor:/root(21)# emerge --update --newuse --deep --with-bdeps=y @world * IMPORTANT: 2 news items need reading for repository 'gentoo'. * Use eselect news to read news items. Calculating dependencies... done! [ebuild U ] dev-util/byacc-20130925 [20130304] [ebuild U ] dev-java/ant-owanttask-1.3.2 [1.1-r12] [ebuild U ] sys-devel/gcc-4.7.3-r1 [4.7.3] [ebuild r U ] dev-util/mdds-0.9.0 [0.8.1] [ebuild rR ] dev-util/mdds-0.8.1 ... [ebuild U ] media-libs/xine-lib-1.2.4 [1.2.3] !!! Multiple package instances within a single package slot have been pulled !!! into the dependency graph, resulting in a slot conflict: dev-util/mdds:0 (dev-util/mdds-0.9.0::gentoo, ebuild scheduled for merge) pulled in by (no parents that aren't satisfied by other packages in this slot) (dev-util/mdds-0.8.1::gentoo, ebuild scheduled for merge) pulled in by =dev-util/mdds-0.8*:= required by (app-office/libreoffice-4.1.2.2::gentoo, installed) >=dev-util/mdds-0.7.1:0/0.8.1= required by (dev-libs/libixion-0.5.0::gentoo, installed) (and 1 more with the same problems) The output of 'emerge --update --newuse --deep --with-bdeps=y --tree --unordered-display @world' is in the attachted file. root@condor:/root(3)# emerge --update --newuse --deep --with-bdeps=y --tree --unordered-display @world emerge --info^C root@condor:/root(3)# emerge --info Portage 2.2.7 (default/linux/amd64/13.0/desktop, gcc-4.7.3, glibc-2.17, 3.11.0-gentoo x86_64) ================================================================= System uname: Linux-3.11.0-gentoo-x86_64-Intel-R-_Core-TM-2_CPU_6600_@_2.40GHz-with-gentoo-2.2 KiB Mem: 7069872 total, 2799692 free KiB Swap: 50347696 total, 50159500 free Timestamp of tree: Fri, 27 Sep 2013 07:00:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 app-shells/bash: 4.2_p45 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.5-r2, 3.2.5-r2, 3.3.2-r2 dev-util/cmake: 2.8.11.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.13.4, 1.14 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.6.4, 4.7.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.11 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo x11 science sunrise lordvan local g-cpan g-octave Installed sets: @system ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /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-php5.3/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.3/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="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" 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 xattr" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ rsync://ftp.fi.muni.cz/pub/linux/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo rsync://gd.tuwien.ac.at/opsys/linux/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo http://gentoo.oregonstate.edu" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" 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_condor" PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/lordvan /usr/local/portage /var/lib/cpan /var/lib/g-octave" USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit cracklib crypt css cuda cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate lirc live lm_sensors lua lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline real reiserfs reports rhythmbox rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core 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 lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps lvm mdraid syslog" DVB_CARDS="tda10045 tda10046lifeview" 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 void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" 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, SYNC, USE_PYTHON
Created attachment 359674 [details] Output of 'emerge --update --newuse --deep --with-bdeps=y --tree --unordered-display @world'
The original problem at "wildcat" is no more visible. Since friday 'emerge --sync && emerge -uvDN --keep-going' was run by cron daemon twice. But there is now a now slot conflict with dev-util/mdds. I will file a separate bug for this.
Okay, you want to package.mask >=dev-util/mdds-0.8.2 until the reverse dependencies allow newer versions; if you are running stable, this might be obtainable by using package.accept_keywords on the reverse dependencies. Relevant parts of the output: [nomerge ] app-office/libreoffice-4.1.2.2 [ebuild rR ] dev-libs/liborcus-0.5.1 [ebuild r U ] dev-util/mdds-0.9.0 [0.8.1] [nomerge ] dev-libs/libixion-0.5.0 [ebuild rR ] dev-util/mdds-0.8.1 =dev-util/mdds-0.8*:= required by (app-office/libreoffice-4.1.2.2::gentoo) >=dev-util/mdds-0.7.1:0/0.8.1= required by (dev-libs/libixion-0.5.0::gentoo) I don't see a real bug here, just conflicting choices; it'll resolve itself in the future as new versions come (or you make them available), I guess...
