When running the command "equery depends" to check the dependencies in the end is reported that has a invalid atom. This happen after the package "gnome-extra/policykit-gnome" has been removed. I try reinstall the package but is not any more in portage. # equery depends policykit * These packages depend on policykit: !!! Invalid atom: '4473' equery depends polkit * These packages depend on polkit: gnome-base/gconf-2.32.0-r1 (policykit ? sys-auth/polkit) gnome-base/gnome-applets-2.32.1.1 (policykit ? >=sys-auth/polkit-0.92) gnome-base/gnome-settings-daemon-2.32.1 (policykit ? >=sys-auth/polkit-0.91) gnome-extra/nm-applet-0.8.2 (>=sys-auth/polkit-0.96-r1) gnome-extra/polkit-gnome-0.99 (>=sys-auth/polkit-0.97) net-misc/modemmanager-0.4_p20101211 (policykit ? >=sys-auth/polkit-0.95) net-misc/networkmanager-0.8.2-r4 (>=sys-auth/polkit-0.92) sys-auth/consolekit-0.4.3 (policykit ? >=sys-auth/polkit-0.96) sys-fs/udisks-1.0.2 (>=sys-auth/polkit-0.97) sys-power/upower-0.9.8 (>=sys-auth/polkit-0.97) !!! Invalid atom: '4473' # revdep-rebuild * Configuring search environment for revdep-rebuild * Checking reverse dependencies * Packages containing binaries and libraries broken by a package update * will be emerged. * Collecting system binaries and libraries * Found existing 1_files.rr * Collecting complete LD_LIBRARY_PATH * Found existing 2_ldpath.rr. * Checking dynamic linking consistency * Found existing 3_broken.rr. * Assigning files to packages * Found existing 4_raw.rr * Cleaning list of packages to rebuild * Found existing 4_pkgs.rr * Assigning packages to ebuilds * Found existing 4_ebuilds.rr * Evaluating package order * Portage could not find any version of the following packages it could build: * gnome-extra/policykit-gnome:0 * (Perhaps they are masked, blocked, or removed from portage.) * Try to emerge them manually. * Warning: Portage cannot rebuild any of the necessary packages. Reproducible: Always Steps to Reproduce: 1. equery depends policykit 2. equery depends polkit 3. Actual Results: !!! Invalid atom: '4473' Portage 2.1.9.35 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.12.2-r0, 2.6.37-gentoo x86_64) ================================================================= System uname: Linux-2.6.37-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7250_@_2.00GHz-with-gentoo-2.0.1 Timestamp of tree: Tue, 01 Feb 2011 18:30:01 +0000 app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r2 dev-lang/python: 2.6.6-r1, 2.7.1, 3.1.3 dev-util/cmake: 2.8.3-r1 sys-apps/baselayout: 2.0.1-r1 sys-apps/openrc: 0.7.0 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.10.3, 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.4.5, 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA AdobeFlash-10.1 AdobeFlash-10" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/openvpn/easy-rsa" 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/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=nocona -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="" GENTOO_MIRRORS="http://rsync.de.gentoo.org/ http://de-mirror.org/distro/gentoo/ http://gentoo.mirror.pw.edu.pl/ http://gentoo.tiscali.nl/" LANG="en_US.UTF-8" LDFLAGS="-Wl,--as-needed" LINGUAS="en pt" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_EXTRA_OPTS="--exclude-from=/etc/portage/rsync_excludes" 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="/usr/portage/local" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdr cli consolekit cracklib crypt cups cxx db dbus dri dts dvd dvdr emboss encode exif fam firefox flac gdbm gdu gif gnome gpm gtk hal iconv jpeg lcms ldap libnotify mad mikmod mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly ogg opengl openmp pam pango pcre pdf perl png policykit ppds pppd python qt3support readline sdl session spell sse sse2 ssl startup-notification svg sysfs tcpd tiff truetype udev unicode usb vorbis x264 xcb xml xorg xulrunner xv xvid zlib" 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 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="evdev keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en pt" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS
Looks like something in /etc/portage is doing this. grep -r 4473 /etc/portage Also, uninstall policykit - it's masked /because/ nothing any longer depends on it.
I have already uninstalled the policykit. Because of this I have this problem! # grep -r 4473 /etc/portage this don't give anything. # emerge --search policykit Searching... [ Results for search key : policykit ] [ Applications found : 0 ] # equery depends policykit * These packages depend on policykit: !!! Invalid atom: '4473'
Anything in /var/lib/portage/world or /usr/portage/local perhaps?
# grep -r 4473 /var/lib/portage/world nothing # grep -r 4473 /usr/portage/local nothing I discovered that this problem happens with any package that I search. # equery depends hal * These packages depend on hal: app-misc/hal-info-20091130 (>=sys-apps/hal-0.5.10) gnome-base/gnome-applets-2.32.1.1 (hal ? >=sys-apps/hal-0.5.3) gnome-base/gnome-vfs-2.24.4 (hal ? >=sys-apps/hal-0.5.7) gnome-base/gvfs-1.6.6-r1 (>=sys-apps/hal-0.5.10) media-gfx/gimp-2.6.11 (hal ? sys-apps/hal) !!! Invalid atom: '4473' # equery depends app-arch/zip * These packages depend on app-arch/zip: cross-avr/gcc-4.2.4-r1 (app-arch/zip) dev-java/ant-core-1.8.1 (source ? app-arch/zip) dev-libs/zziplib-0.13.60 (test ? app-arch/zip) media-gfx/hugin-2010.4.0 (app-arch/zip) net-libs/xulrunner-1.9.2.13-r1 (app-arch/zip) sys-devel/gcc-4.4.5 (app-arch/zip) sys-devel/gcc-4.5.2 (app-arch/zip) !!! Invalid atom: '4473' # equery depends jpeg * These packages depend on jpeg: app-editors/xemacs-21.5.29-r2 (jpeg ? virtual/jpeg) app-text/ghostscript-gpl-9.00 (virtual/jpeg) app-text/poppler-0.16.2 (jpeg ? virtual/jpeg) dev-dotnet/libgdiplus-2.8.1 (virtual/jpeg) dev-java/icedtea6-bin-1.9 (>=media-libs/jpeg-8) dev-python/imaging-1.1.7 (virtual/jpeg) media-gfx/autopano-sift-C-2.5.1 (virtual/jpeg) media-gfx/enblend-4.0 (virtual/jpeg) media-gfx/feh-1.11.1 (virtual/jpeg) media-gfx/gimp-2.6.11 (jpeg ? virtual/jpeg) media-gfx/graphviz-2.26.3-r3 (virtual/jpeg) media-gfx/hugin-2010.4.0 (virtual/jpeg) media-gfx/imagemagick-6.6.5.6 (jpeg ? virtual/jpeg) media-gfx/splashutils-1.5.4.3-r3 (>=media-libs/jpeg-6b:0[static-libs]) media-gfx/xv-3.10a-r15 (jpeg ? >=media-libs/jpeg-6b) media-libs/gd-2.0.35-r2 (jpeg ? virtual/jpeg) media-libs/gegl-0.1.2 (jpeg ? virtual/jpeg) media-libs/imlib2-1.4.4 (jpeg ? virtual/jpeg) media-libs/lcms-1.19 (jpeg ? virtual/jpeg) media-libs/lcms-2.1 (jpeg ? virtual/jpeg) media-libs/libmng-1.0.10 (virtual/jpeg) media-libs/libpano13-2.9.17 (virtual/jpeg) media-libs/netpbm-10.51.00-r1 (jpeg ? virtual/jpeg) media-libs/tiff-4.0.0_beta6 (jpeg ? virtual/jpeg) net-libs/xulrunner-1.9.2.13-r1 (virtual/jpeg) net-misc/tightvnc-1.3.10-r1 (media-libs/jpeg) net-misc/vino-2.32.1 (jpeg ? virtual/jpeg:0) net-print/cups-1.4.6 (jpeg ? virtual/jpeg:0) virtual/jpeg-0 (media-libs/jpeg:0) !!! Invalid atom: '4473'
Which version of app-portage/gentoolkit is that?
(In reply to comment #5) > Which version of app-portage/gentoolkit is that? > app-portage/gentoolkit Latest version available: 0.3.0_rc11-r3 Latest version installed: 0.3.0_rc11-r3
I reemerge the gentoolkit but the problem remains. >>> Installing (1 of 1) app-portage/gentoolkit-0.3.0_rc11-r3 * Compilation and optimization of Python modules for CPython 2.7 ... [ ok ] * Compilation and optimization of Python modules for CPython 3.1 ... [ ok ] * * For further information on gentoolkit, please read the gentoolkit * guide: http://www.gentoo.org/doc/en/gentoolkit.xml * * Another alternative to equery is app-portage/portage-utils >>> Auto-cleaning packages... >>> No outdated packages were found on your system. * GNU info directory index is up-to-date. # equery depends gentoolkit * These packages depend on gentoolkit: !!! Invalid atom: '4473'
Do the grep on /var/db/pkg since that is where equery searches
(In reply to comment #8) > Do the grep on /var/db/pkg since that is where equery searches > I get a lot of lines with the string '4473'. It's safe remove this directory? /var/db/pkg/app-office/dia-0.97.1/CONTENTS:obj /usr/share/dia/shapes/Cybernetics/factor-greater1.shape 1a1156ae447368066d2a3e350c7b9ed1 1290988383 /var/db/pkg/app-office/dia-0.97.1/CONTENTS:obj /usr/share/dia/shapes/Lights/Structure.png e5763bee8a4ee346f6688f09f24473b0 1290988383 /var/db/pkg/app-office/dia-0.97.1/CONTENTS:obj /usr/share/gnome/help/dia/en/graphics/file-preferences-ui.png 14e66cd26328a44f3a8c7f4473952f11 1290988387 /var/db/pkg/app-office/dia-0.97.1/CONTENTS:obj /usr/share/gnome/help/dia/en/graphics/polyline-rightclick.png 9bdae421323093c34473d7574212e399 1290988387 ...
No no do NOT remove it, just wanted to see if there was a particular file that was corrupt in which case reinstalling the corresponding package should make equery happy
Suggestion, try 'grep -w' to avoid getting false hits on all those checksums with this number as a substring
(In reply to comment #11) > Suggestion, try 'grep -w' to avoid getting false hits on all those checksums > with this number as a substring > Ok, I found one. # grep -rw 4473 /var/db/pkg Binary file /var/db/pkg/virtual/perl-Scalar-List-Utils-1.21/RDEPEND matches # more /var/db/pkg/virtual/perl-Scalar-List-Utils-1.21/RDEPEND matches 4473 I reemerge the package. # emerge virtual/perl-Scalar-List-Utils And the problem remains. # equery depends gentoolkit * These packages depend on gentoolkit: !!! Invalid atom: '4473' When I tried to remove the package happened this: # emerge -C virtual/perl-Scalar-List-Utils * This action can remove important packages! In order to be safer, use * `emerge -pv --depclean <atom>` to check for reverse dependencies before * removing packages. virtual/perl-Scalar-List-Utils selected: 1.21 1.23 protected: none omitted: none All selected packages: virtual/perl-Scalar-List-Utils-1.23 virtual/perl-Scalar-List-Utils-1.21 >>> 'Selected' packages are slated for removal. >>> 'Protected' and 'omitted' packages will not be removed. >>> Waiting 5 seconds before starting... >>> (Control-C to abort)... >>> Unmerging in: 5 4 3 2 1 >>> Unmerging virtual/perl-Scalar-List-Utils-1.23... >>> Unmerging virtual/perl-Scalar-List-Utils-1.21... !!! FAILED prerm: /var/db/pkg/virtual/perl-Scalar-List-Utils-1.21/EAPI Unable to do any operations on 'virtual/perl-Scalar-List-Utils-1.21', since its EAPI is higher than this portage version's. Please upgrade to a portage version that supports EAPI '+'. But the problem disappeared. # equery depends gentoolkit * These packages depend on gentoolkit: I reemerge the package. # emerge virtual/perl-Scalar-List-Utils # equery depends gentoolkit * These packages depend on gentoolkit: # equery depends perl-Scalar-List-Utils * These packages depend on perl-Scalar-List-Utils: app-editors/padre-0.800 (>=virtual/perl-Scalar-List-Utils-1.18) dev-perl/Class-Adapter-1.07 (>=virtual/perl-Scalar-List-Utils-1.10) dev-perl/Class-MOP-1.120 (>=virtual/perl-Scalar-List-Utils-1.18) dev-perl/Devel-Dumpvar-1.06 (>=virtual/perl-Scalar-List-Utils-1.18) dev-perl/IO-Socket-SSL-1.380 (virtual/perl-Scalar-List-Utils) dev-perl/Moose-1.21 (>=virtual/perl-Scalar-List-Utils-1.19) dev-perl/PPI-1.213 (>=virtual/perl-Scalar-List-Utils-1.20) dev-perl/PPIx-Regexp-0.16 (virtual/perl-Scalar-List-Utils) dev-perl/Params-Util-1.03 (>=virtual/perl-Scalar-List-Utils-1.18) dev-perl/Pod-Abstract-0.20 (virtual/perl-Scalar-List-Utils) dev-perl/Thread-Queue-2.11 (virtual/perl-Scalar-List-Utils) dev-perl/Thread-Semaphore-2.11 (virtual/perl-Scalar-List-Utils) perl-core/IO-Compress-2.33 (virtual/perl-Scalar-List-Utils) perl-core/Math-BigInt-1.99 (>=virtual/perl-Scalar-List-Utils-1.14) Permanently the problem disappeared :-) Thanks guys for the help.
