After a month or two I synced my portage tree. I see the following broken filenames in revdep-rebuild output: # revdep-rebuild -i * 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 * Generated new 1_files.rr * Collecting complete LD_LIBRARY_PATH * Generated new 2_ldpath.rr * Checking dynamic linking consistency [ 13% ] * broken /usr/bin/copy_db (requires libtcl8.5.so) [ 35% ] * broken /usr/bin/tg_index.bin (requires libtcl8.5.so libtk8.5.so) * broken /usr/bin/tg_view.bin (requires libtcl8.5.so libtk8.5.so) [ 40% ] * broken /usr/lib32/egl/egl_gallium.so (requires libudev.so.1) [ 45% ] * broken /usr/lib32/opengl/xorg-x11/lib/libEGL.so.1.0.0 (requires libudev.so.1) [ 68% ] * broken /usr/lib64/libreflapacke.so (requires liblapack.so) [ 86% ] * broken /usr/lib64/staden/libcopy_reads.so (requires libtcl8.5.so) * broken /usr/lib64/staden/libgap.so (requires libtcl8.5.so libtk8.5.so) * broken /usr/lib64/staden/libgap5.so (requires libtcl8.5.so libtk8.5.so) * broken /usr/lib64/staden/libhaplo.so (requires libtcl8.5.so) * broken /usr/lib64/staden/libprefinish.so (requires libtcl8.5.so) * broken /usr/lib64/staden/libspin.so (requires libtcl8.5.so libtk8.5.so) * broken /usr/lib64/staden/libtk_utils.so (requires libtcl8.5.so libtk8.5.so) [ 100% ] * broken /usr/lib64/firefox/libxpcom.so (no version information available) * broken /usr/lib64/firefox/plugin-container (no version information available) * broken /usr/lib64/seamonkey-devel/sdk/bin/xpcshell (no version information available) * broken /usr/lib64/seamonkey-devel/sdk/lib/libxpcom.so (no version information available) * broken /usr/lib64/seamonkey/libxpcom.so (no version information available) * broken /usr/lib64/seamonkey/plugin-container (no version information available) * Generated new 3_broken.rr * Assigning files to packages * /usr/bin/copy_db -> sci-biology/staden * /usr/bin/tg_index.bin -> sci-biology/staden * /usr/bin/tg_view.bin -> sci-biology/staden * /usr/lib32/egl/egl_gallium.so -> app-emulation/emul-linux-x86-opengl-20130224 /var/db/pkg/app-emulation/-MERGING-emul-linux-x86-opengl * /usr/lib32/opengl/xorg-x11/lib/libEGL.so.1.0.0 -> app-emulation/emul-linux-x86-opengl-20130224 /var/db/pkg/app-emulation/-MERGING-emul-linux-x86-opengl * /usr/lib64/firefox/libxpcom.so -> www-client/firefox * /usr/lib64/firefox/plugin-container -> www-client/firefox * /usr/lib64/libreflapacke.so -> /var/db/pkg/sci-libs/-MERGING-lapacke-reference * /usr/lib64/seamonkey-devel/sdk/bin/xpcshell -> www-client/seamonkey * /usr/lib64/seamonkey-devel/sdk/lib/libxpcom.so -> www-client/seamonkey * /usr/lib64/seamonkey/libxpcom.so -> www-client/seamonkey * /usr/lib64/seamonkey/plugin-container -> www-client/seamonkey * /usr/lib64/staden/libcopy_reads.so -> sci-biology/staden * /usr/lib64/staden/libgap.so -> sci-biology/staden * /usr/lib64/staden/libgap5.so -> sci-biology/staden * /usr/lib64/staden/libhaplo.so -> sci-biology/staden * /usr/lib64/staden/libprefinish.so -> sci-biology/staden * /usr/lib64/staden/libspin.so -> sci-biology/staden * /usr/lib64/staden/libtk_utils.so -> sci-biology/staden * Generated new 4_raw.rr and 4_owners.rr * Cleaning list of packages to rebuild * Generated new 4_pkgs.rr * Assigning packages to ebuilds /usr/bin/revdep-rebuild: line 910: /var/db/pkg//var/db/pkg/app-emulation/-MERGING-emul-linux-x86-opengl-20121202-r1/CONTENTS/SLOT: No such file or directory /usr/bin/revdep-rebuild: line 910: /var/db/pkg//var/db/pkg/sci-libs/-MERGING-lapacke-reference-3.4.2/CONTENTS/SLOT: No such file or directory * Generated new 4_ebuilds.rr * Evaluating package order ERROR: Invalid atom: '/var/db/pkg/app-emulation/-MERGING-emul-linux-x86-opengl:' ERROR: Invalid atom: '/var/db/pkg/sci-libs/-MERGING-lapacke-reference:' Invalid ebuild name: /home/mmokrejs/proj/sci/sci-biology/staden/staden-svn2923.ebuild * Generated new 5_order.rr * All prepared. Starting rebuild emerge --complete-graph=y --oneshot app-emulation/emul-linux-x86-opengl:0 sci-biology/staden:0 www-client/firefox:0 www-client/seamonkey:0 .......... [cut] Portage 2.1.11.54 (default/linux/amd64/10.0, gcc-4.6.3, glibc-2.16.0, 3.7.10-default x86_64) ================================================================= System uname: Linux-3.7.10-default-x86_64-Intel-R-_Core-TM-_i7-2640M_CPU_@_2.80GHz-with-gentoo-2.2 KiB Mem: 16329496 total, 6681184 free KiB Swap: 4998972 total, 4998756 free Timestamp of tree: Mon, 04 Mar 2013 13:00:01 +0000 ld GNU ld (GNU Binutils) 2.23.1 app-shells/bash: 4.2_p42 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.5.4-r5, 2.6.8-r1, 2.7.3-r3, 3.2.3-r2 dev-util/cmake: 2.8.10.2-r1 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.11.8 sys-apps/sandbox: 2.6 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.11.6, 1.12.6 sys-devel/binutils: 2.23.1 sys-devel/gcc: 4.2.4-r1, 4.3.6-r1, 4.5.4, 4.6.3, 4.7.2-r1 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.8 (virtual/os-headers) sys-libs/glibc: 2.16.0 Repositories: gentoo gentoo-haskell science x-portage x-layman ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4 -mavx -maes -march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa" CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/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 -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -msse4 -mavx -maes -march=native" DISTDIR="/mnt/1TB/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news nostrip parallel-fetch protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" 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="/mnt/1TB/usr/portage" PORTDIR="/mnt/1TB/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/haskell /home/mmokrejs/proj/sci /usr/local/portage /var/lib/layman" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acl acpi alsa amd64 amr apache apache2 berkdb bluetooth bzip2 cairo cgi cli cracklib crypt cups cxx dbus device-mapper dhcp dri emboss encode fax ffmpeg flac fontconfig fortran gd gdbm gimp gpm gtk gudev hal hpijs hwdb iconv id3tag innodb java jce jpeg jpg keymap ladspa laptop lcms libnotify lm_sensors mad mmx modules mpi mpich2 multilib mysql ncurses nfs nls nptl nptlonly nsplugin ntfsprogs ocr ogg opengl openmp openssl pam parport pcre pdf perl php png policykit ppds pppd python readline resolvconf scanner server session sndfile sqlite sse sse2 sse3 ssl suexec svg syslog tcpd threads tiff tk truetype udev unicode usb vim-syntax wavpack x11 xml xorg zlib" ABI_X86="64" 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="authn_core authz_core socache_shmcb unixd 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" 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" 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" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en cs cz" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915 i965 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, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
It's safe to remove these: /var/db/pkg/sci-libs/-MERGING-lapacke-reference /var/db/pkg/app-emulation/-MERGING-emul-linux-x86-opengl They are temporary (lock) files that should have been removed automatically. I have only seen these after catastrophic system failures, myself.
*** This bug has been marked as a duplicate of bug 192778 ***
