РЕШЕНО emerge -avuDN system 'dev-db/-MERGING-libpq:4' is not a valid package atom.

и не знаю чем это поможет, но вот

hunter german # emerge -pvuDN world

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild N ] dev-lang/php-5.3.3-r1 USE="apache2 berkdb bzip2 cgi cli crypt ctype curl curlwrappers exif fileinfo filter ftp gd gdbm hash iconv imap ipv6 json kerberos ldap ldap-sasl mysql mysqli nls odbc pdo phar posix postgres readline session simplexml snmp sockets spell ssl threads tidy tokenizer truetype unicode xml xmlreader xmlwriter xsl zip zlib (-adabas) -bcmath (-birdstep) -calendar -cdb -cjk -concurrentmodphp -db2 (-dbmaker) -debug -doc -embed (-empress) (-empress-bcs) -enchant (-esoob) (-firebird) -flatfile -fpm (-frontbase) -gd-external -gmp -inifile -interbase -intl -iodbc -kolab -libedit -mssql -mysqlnd -oci8 -oci8-instant-client -pcntl -pic -qdbm -recode -sapdb -sharedext -sharedmem -soap (-solid) -sqlite -sqlite3 -suhosin (-sybase-ct) -sysvipc -wddx -xmlrpc -xpm" 0 kB
[ebuild NS ] virtual/httpd-php-5.3 [5.2] 0 kB
[ebuild U ] dev-php/PEAR-PEAR-1.9.1-r1 [1.9.0] 0 kB
[ebuild NS ] mail-client/roundcube-0.4.2 [0.3.1] USE="ldap mysql postgres spell ssl vhosts" 0 kB
[ebuild NS ] dev-db/phpmyadmin-3.3.8.1 [3.3.7] USE="vhosts" 0 kB
[ebuild U ] dev-java/java-config-2.1.11-r1 [2.1.11] 0 kB
[ebuild U ] sys-fs/ntfs3g-2010.8.8 [2010.3.6] USE="acl external-fuse hal -debug -suid -udev" 0 kB
[ebuild U ] net-print/cups-1.4.5 [1.4.4-r2] USE="X acl dbus gnutls jpeg ldap pam perl png python samba ssl threads tiff usb -debug -java -kerberos -php* -slp -static-libs -xinetd" LINGUAS="ru -da -de -es -eu -fi -fr -id -it -ja -ko -nl -no -pl -pt -pt_BR -sv -zh -zh_TW" 0 kB
[ebuild U ] net-fs/samba-3.5.6 [3.5.5] USE="acl client cups fam ldap netapi pam readline server smbclient -addns -ads -aio -avahi -caps -cluster -debug -doc -examples -ldb -quota -smbsharemodes -swat -syslog -winbind" 0 kB
[ebuild U ] net-wireless/bluez-4.75 [4.69] USE="alsa cups usb -attrib% -caps -consolekit -debug -gstreamer -health% -maemo6 -old-daemons -pcmcia -pnat% -test-programs" 0 kB
[ebuild U ] dev-java/icedtea6-bin-1.9.1 [1.8.1] USE="X alsa nsplugin -doc -examples -source" 0 kB
[ebuild U ] dev-python/pygtk-2.17.0 [2.16.0-r1] USE="-doc -examples -test" 0 kB
[ebuild U ] www-client/chromium-8.0.552.215 [7.0.517.13] USE="cups gecko-mediaplayer%* -gnome -gnome-keyring -system-sqlite% (-system-v8)" 0 kB
[ebuild U ] x11-libs/qt-gui-4.6.3-r2 [4.6.3] USE="accessibility cups dbus exceptions glib mng qt3support tiff (-aqua) -debug -gtk -nas -nis -pch -raster -trace -xinerama" 0 kB
[ebuild U ] games-board/pokerth-0.8.1 [0.7.1] USE="-dedicated" 0 kB
[ebuild U ] media-libs/taglib-1.6.3 [1.6.1-r1] USE="asf mp4 -debug -examples -test" 0 kB
[ebuild U ] app-text/poppler-0.14.4 [0.14.1] USE="abiword cairo cxx jpeg jpeg2k lcms png qt4 utils xpdf-headers -cjk -curl -debug -doc -exceptions" 0 kB
[ebuild U ] media-sound/qmmp-0.4.3 [0.4.2] USE="aac alsa dbus ffmpeg flac hal kde mad vorbis -bs2b -cdda -cover -enca -jack -ladspa -libsamplerate -lyrics -mms -modplug -mplayer -mpris -musepack -notifier -oss -projectm -pulseaudio -scrobbler -sndfile -tray -wavpack" 0 kB
[ebuild U ] media-video/xvideoservicethief-2.4.1 [2.4] USE="-debug -doc" LINGUAS="ru -br -ca -cs -da -de -es -fr -gl -hu -it -ja -ko -nl -pl -ro -sv" 0 kB
[ebuild U ] net-im/centerim-4.22.9 [4.22.7-r1] USE="aim crypt icq irc jabber jpeg msn nls ssl yahoo -bidi -gadu -lj -otr -rss" 0 kB
[ebuild U ] kde-base/libkexiv2-4.4.5-r1 [4.4.5] USE="(-aqua) -debug (-kdeenablefinal) (-kdeprefix)" 0 kB
[ebuild U ] kde-base/libkdcraw-4.4.5-r1 [4.4.5] USE="(-aqua) -debug (-kdeenablefinal) (-kdeprefix)" 0 kB
[ebuild U ] net-libs/libktorrent-1.0.4 [1.0.3] USE="(-aqua) -debug -doc (-kdeenablefinal)" LINGUAS="ru uk -ar -ast -be -bg -ca -ca@valencia -cs -da -de -el -en_GB -eo -es -et -eu -fi -fr -ga -gl -hi -hne -hr -hu -is -it -ja -km -ku -lt -lv -ms -nb -nds -nl -nn -oc -pl -pt -pt_BR -ro -se -si -sk -sl -sr -sr@ijekavian -sr@ijekavianlatin -sr@latin -sv -tr -zh_CN -zh_TW" 0 kB
[ebuild U ] kde-base/gwenview-4.4.5-r1 [4.4.5] USE="handbook (-aqua) -debug (-kdeenablefinal) (-kdeprefix) -kipi -semantic-desktop" 0 kB
[ebuild U ] sys-block/partitionmanager-1.0.3 [1.0.1] USE="(-aqua) -debug (-kdeenablefinal)" LINGUAS="ru uk -bg -ca -da -de -el -en_GB -es -et -fr -gl -ja -lt -nb -nds -nl -nn -pa -pl -pt -pt_BR -ro -sv -tr -zh_CN -zh_TW" 0 kB
[ebuild U ] kde-base/krdc-4.4.5-r1 [4.4.5] USE="handbook jpeg zeroconf (-aqua) -debug (-kdeenablefinal) (-kdeprefix) -rdp -vnc" 0 kB
[ebuild U ] media-sound/amarok-2.3.2-r1 [2.3.1.90] USE="opengl player utils -cdda -daap -debug -embedded -ipod (-kdeenablefinal) -lastfm -mp3tunes -mtp -semantic-desktop" LINGUAS="ru uk -af -bg -ca -ca@valencia -cs -da -de -el -en_GB -es -et -fr -it -ja -lt -lv -nb -nds -pa -pl -pt -pt_BR -sk -sl -sr -sr@ijekavian -sr@ijekavianlatin -sr@latin -sv -th -tr -zh_CN -zh_TW" 0 kB
[ebuild U ] net-p2p/ktorrent-4.0.4 [4.0.3] USE="bwscheduler downloadorder infowidget ipfilter kross logviewer magnetgenerator mediaplayer scanfolder search shutdown stats upnp zeroconf (-aqua) -debug (-kdeenablefinal) -plasma -rss -webinterface" LINGUAS="ru uk -ar -ast -be -bg -ca -ca@valencia -cs -da -de -el -en_GB -eo -es -et -eu -fi -fr -ga -gl -hi -hne -hr -hu -is -it -ja -km -lt -lv -mai -ms -nb -nds -nl -nn -oc -pl -pt -pt_BR -ro -se -si -sk -sl -sr -sr@ijekavian -sr@ijekavianlatin -sr@latin -sv -tr -zh_CN -zh_TW" 0 kB
[ebuild U ] net-libs/xulrunner-1.9.2.13 [1.9.2.9] USE="alsa dbus ipc libnotify startup-notification -custom-optimization -debug -gnome -java -system-sqlite -wifi (-cups%*)" 50,288 kB
[ebuild U ] mail-client/thunderbird-3.1.7 [3.1.3] USE="alsa dbus ldap libnotify lightning startup-notification -bindist -crypt -custom-optimization -gnome -mozdom -system-sqlite -wifi (-cups%*)" LINGUAS="ru uk -af -ar -be -bg -bn -bn_BD -ca -cs -da -de -el -en -en_GB -en_US -es -es_AR -es_ES -et -eu -fi -fr -fy -fy_NL -ga -ga_IE -he -hu -id -is -it -ja -ko -lt -nb -nb_NO -nl -nn -nn_NO -pa -pa_IN -pl -pt -pt_BR -pt_PT -ro -si -sk -sl -sq -sv -sv_SE -tr -zh -zh_CN -zh_TW" 64,839 kB
[ebuild U ] www-client/firefox-3.6.13 [3.6.9-r1] USE="alsa dbus ipc libnotify startup-notification -bindist -custom-optimization -gnome -java -system-sqlite -wifi (-cups%*)" LINGUAS="ru uk -af -ar -as -be -bg -bn -bn_BD -bn_IN -ca -cs -cy -da -de -el -en -en_GB -en_US -eo -es -es_AR -es_CL -es_ES -es_MX -et -eu -fa -fi -fr -fy -fy_NL -ga -ga_IE -gl -gu -gu_IN -he -hi -hi_IN -hr -hu -id -is -it -ja -ka -kk -kn -ko -ku -lt -lv -mk -ml -mr -nb -nb_NO -nl -nn -nn_NO -oc -or -pa -pa_IN -pl -pt -pt_BR -pt_PT -rm -ro -si -sk -sl -sq -sr -sv -sv_SE -ta -ta_LK -te -th -tr -vi -zh_CN -zh_TW" 268 kB
[ebuild U ] app-office/openoffice-3.2.1-r1 [3.2.0] USE="cups dbus kde ldap nsplugin opengl pam (-aqua) -bash-completion -binfilter -debug -eds -gnome -gstreamer -gtk -java (-kdeenablefinal) -odk -templates (-mono%)" LINGUAS="ru uk -af -ar -as_IN -be_BY -bg -bn -br -brx -bs -ca -cs -cy -da -de -dgo -dz -el -en -en_GB -en_US -en_ZA -eo -es -et -eu -fa -fi -fr -ga -gl -gu -he -hi_IN -hr -hu -id -it -ja -ka -kk -km -kn_IN -ko -kok -ks -ku -lt -mai -mk -ml_IN -mn -mni -mr_IN -nb -ne -nl -nn -nr -ns -oc -or_IN -pa_IN -pl -pt -pt_BR -rw -sa_IN -sat -sd -sh -sk -sl -sr -ss -st -sv -sw_TZ -ta -ta_IN -te_IN -tg -th -ti_ER -tn -tr -ts -ur_IN -uz -ve -vi -xh -zh_CN -zh_TW -zu" 0 kB
[ebuild U ] media-gfx/imagemagick-6.6.5.6 [6.6.3.0] USE="X bzip2 corefonts cxx djvu jpeg jpeg2k lcms openmp png svg tiff truetype xml zlib -autotrace -fftw -fontconfig -fpx -graphviz -gs -hdri -jbig -lqr -openexr -perl -q32 -q8 -raw -static-libs -wmf" VIDEO_CARDS="nvidia" 0 kB
[ebuild N ] media-plugins/kipi-plugins-1.2.0-r2 USE="cdr crypt imagemagick mjpeg opengl (-aqua) -calendar -debug -expoblending -ipod (-kdeenablefinal) -redeyes -scanner" LINGUAS="ru uk -ar -be -ca -cs -da -de -el -en_GB -es -et -fi -fr -ga -gl -hi -hne -is -it -ja -km -lt -lv -ms -nb -nds -nl -nn -oc -pa -pl -pt -pt_BR -ro -se -sk -sv -th -tr -zh_CN -zh_TW" 0 kB
[ebuild U ] app-office/koffice-data-2.2.2 [2.1.0] USE="(-aqua) (-kdeenablefinal)" 0 kB
[ebuild U ] app-office/koffice-libs-2.2.2 [2.1.0] USE="crypt opengl (-aqua) -debug (-kdeenablefinal) -openexr -reports% -test" 0 kB
[ebuild U ] media-gfx/digikam-1.2.0-r3 [1.1.0-r1] USE="addressbook geolocation gphoto2 thumbnails (-aqua) -debug -doc -handbook% (-kdeenablefinal) -lensfun -semantic-desktop -video% (-glib%*)" LINGUAS="ru uk -ar -be -bg -ca -cs -da -de -el -es -et -eu -fa -fi -fr -ga -gl -he -hi -is -it -ja -km -ko -lb% -lt -lv -nds -ne -nl -nn -pa -pl -pt -pt_BR -ro -se -sk -sl -sv -th -tr -vi -zh_CN -zh_TW (-ca@valencia%) (-en_GB%) (-eo%) (-hne%) (-hr%) (-hu%) (-nb%)" 0 kB
[ebuild U ] www-plugins/adobe-flash-10.2.161.23_pre20101117 [10.2.161.22_pre20100915] USE="32bit 64bit (multilib) nspluginwrapper" 0 kB
[ebuild U ] app-office/kword-2.2.2 [2.1.0] USE="(-aqua) -debug (-kdeenablefinal) -wpd (-wv2%*)" 0 kB
[uninstall ] app-text/wv2-0.4.2 USE="zlib"
[blocks b ] app-text/wv2 ("app-text/wv2" is blocking app-office/kword-2.2.2)

Total: 39 packages (34 upgrades, 2 new, 3 in new slots, 1 uninstall), Size of downloads: 115,393 kB
Conflict: 1 block

!!! The following installed packages are masked:
- sys-apps/slocate-3.1-r1 (masked by: package.mask)
/usr/portage/profiles/package.mask:
# Samuli Suominen (14 Nov 2010)
# No longer developed and replaced by sys-apps/mlocate
# Bug 338380
# Removal in 30 days

For more information, see the MASKED PACKAGES section in the emerge
man page or refer to the Gentoo Handbook.

* IMPORTANT: 4 news items need reading for repository 'gentoo'.
* Use eselect news to read news items.

Удалите оба каталога и попробуйте обновиться снова.

просто параллельно работал paludis, который на момент компиляции создаёт записи вида /var/db/pkg/dev-db/-MERGING-libpq-8.1.11 /var/db/pkg/media-fonts/-MERGING-gnu-gs-fonts-std-8.1 , а после успешной сборки их переименовывает в нормальные.
Если сборка не получилась, то они так и останутся висеть в /var/db/pkg. Их можно просто удалить: rm -rf /var/db/pkg/dev-db/-MERGING-libpq-8.1.11 /var/db/pkg/media-fonts/-MERGING-gnu-gs-fonts-std-8.11
Потом если что, можно пересоздать базу пакетов через emerge --regen; или переустановить эти пакеты палудисом.