Since a week when I always execute "emerge -u world" the program shows the following messages: !!! Invalid db entry: /var/db/pkg//x11-base !!! Invalid db entry: /var/db/pkg//x11-libs !!! Invalid db entry: /var/db/pkg//x11-misc !!! Invalid db entry: /var/db/pkg//www-client !!! Invalid db entry: /var/db/pkg//x11-terms !!! Invalid db entry: /var/db/pkg//app-admin !!! Invalid db entry: /var/db/pkg//app-crypt !!! Invalid db entry: /var/db/pkg//x11-themes !!! Invalid db entry: /var/db/pkg//perl-core !!! Invalid db entry: /var/db/pkg//gnome-base !!! Invalid db entry: /var/db/pkg//mail-mta !!! Invalid db entry: /var/db/pkg//app-arch !!! Invalid db entry: /var/db/pkg//app-i18n !!! Invalid db entry: /var/db/pkg//app-text !!! Invalid db entry: /var/db/pkg//sys-devel !!! Invalid db entry: /var/db/pkg//dev-db !!! Invalid db entry: /var/db/pkg//net-nds !!! Invalid db entry: /var/db/pkg//media-libs !!! Invalid db entry: /var/db/pkg//sys-process !!! Invalid db entry: /var/db/pkg//sys-apps !!! Invalid db entry: /var/db/pkg//sys-libs !!! Invalid db entry: /var/db/pkg//net-fs !!! Invalid db entry: /var/db/pkg//net-mail !!! Invalid db entry: /var/db/pkg//net-misc !!! Invalid db entry: /var/db/pkg//net-print !!! Invalid db entry: /var/db/pkg//dev-java !!! Invalid db entry: /var/db/pkg//dev-lang !!! Invalid db entry: /var/db/pkg//dev-libs !!! Invalid db entry: /var/db/pkg//dev-perl !!! Invalid db entry: /var/db/pkg//dev-util !!! Invalid db entry: /var/db/pkg//dev-python !!! Invalid db entry: /var/db/pkg//app-editors !!! Invalid db entry: /var/db/pkg//sys-fs !!! Invalid db entry: /var/db/pkg//app-shells !!! Invalid db entry: /var/db/pkg//media-fonts I've tried to use /usr/lib/portage/bin/./fix-db.py to solve that issue as it was suggested in the forums, but it didn't work. I've also completely deleted all directories in /var/db/pkg and then ran emerge to reinstall the entire system but it hasn't worked too.
I've found that this issue seems to be very similar to the previous bug #31881 that has been closed about two years ago.
you neglected to post `emerge info` like the bug report page told you to
*** Bug 107066 has been marked as a duplicate of this bug. ***
post the info here and re-open, dont file a new bug report
Portage 2.0.52-r1 (default-linux/x86/2005.0, gcc-3.4.4, glibc-2.3.5-r1, 2.6.13 i686) ================================================================= System uname: 2.6.13 i686 Intel(R) Pentium(R) 4 CPU 3.00GHz Gentoo Base System version 1.12.0_pre8 ccache version 2.4 [enabled] dev-lang/python: 2.4.1-r1 sys-apps/sandbox: 1.2.13 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6 sys-devel/binutils: 2.16.1 sys-devel/libtool: 1.5.20 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=pentium4 -O2 -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/texmf/web2c /etc/env.d" CXXFLAGS="-march=pentium4 -O2 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache distlocks nostrip sandbox sfperms strict userpriv usersandbox" GENTOO_MIRRORS="http://www.die.unipd.it/pub/Linux/distributions/gentoo-sources/ http://gentoo.osuosl.org/ ftp://ftp.unina.it/pub/linux/distributions/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo" LINGUAS="en it" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage_overlay" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="x86 3dnow X acl alsa apache2 apm arts avi bash-completion berkdb bitmap-fonts crypt cups doc dvd eds emacs emboss encode ethereal examples expat fam foomaticdb fortran gcj gd gd-external gdbm gif gnome gpm gstreamer gtk gtk2 imlib ipv6 java javascript jpeg jpg kde libg++ libwww mad mikmod mime mmap mmx mono motif mp3 mpeg mpi msn mysql mysqli ncurses nls nptl ogg oggvorbis opengl openssh openssl oss pam pdflib perl php pic png posix postgres python qt quicktime readline samba sdl sharedmem sockets spell sqlite sse ssh ssl sysv5ipc tcltk tcpd tiff truetype truetype-fonts type1-fonts vorbis wxwindows xml2 xmms xsl xv zlib linguas_en linguas_it userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS
Err... you nuked /var/db/pkg ? Doing that wipes portage's knowledge of *alL* packages. If that directory is nuked, and you're still getting those errors, I'd wonder about fs corruption. If you have restored /var/db/pkg , tarball it and post it here.
Sorry if I have been unable to explain properly due to my poor English. Yes I had deleted all the /var/db/pkg subdirectories but then I ran "emerge -e system", "emerge --sync" and "emerge -uD world" to rebuild them. While the directory was empty there weren't any error. After re-emerging the entire system those "Invalid db entry in /var/db/pkg" errors appeared again. I must exclude any filesystem problem because I have mounted /var in a new formatted disk partition before emerging like above-mentioned. I had build a file.tar.bz2 with the whole content of /var/db/pkg, but bugzilla didn't accept it because it is too large (6MB). What else can I do?
post it in webspace, or tarball up a selection of nodes that are being flagged.
Created attachment 69236 [details] selection of subdirectories from /var/db/pkg as requested I have uploaded a selection of subdirectories from /var/db/pkg in a 1.6MB file.tar.bz2 (selection_from_var-db-pkg.tar.bz2) as you requested. I have merely chosen the first 16 over 36 subdirectories as they are listed when errors are reported at execution of "emerge -u world". If and when you would need the other ones, please ask.
Any news about this bug? A new problem has been added to the one already reported with the portage upgrade to the new release 2.0.53_rc3. When running "emerge -u world" some more messages are now shown besides the ones that I've already reported. New messages say that many packages are not installed, even though they are. It seems that directories with "Invalid db entry" match the ones it says packages are not installed. I have tried to "emerge --unmerge <package>" and then a new "emerge <package", but these issues have not been fixed that way. I would really appreciate you to fix these annoying bugs. Thank you. # emerge -uD world *** Package in world file is not installed: app-forensics/chkrootkit *** Package in world file is not installed: dev-db/mysql++ *** Package in world file is not installed: sys-auth/pam_mysql *** Package in world file is not installed: dev-ada/adabindx *** Package in world file is not installed: dev-php/adodb *** Package in world file is not installed: app-portage/mirrorselect *** Package in world file is not installed: net-analyzer/netcat *** Package in world file is not installed: dev-util/monodoc *** Package in world file is not installed: sys-apps/lshw *** Package in world file is not installed: net-analyzer/snort *** Package in world file is not installed: app-admin/syslog-ng *** Package in world file is not installed: sys-power/acpid *** Package in world file is not installed: app-cdr/cdrtools *** Package in world file is not installed: dev-util/kdoc *** Package in world file is not installed: dev-util/yacc *** Package in world file is not installed: sys-apps/ddcxinfo-knoppix *** Package in world file is not installed: app-forensics/aide *** Package in world file is not installed: dev-util/valgrind *** Package in world file is not installed: sys-fs/reiserfsprogs *** Package in world file is not installed: sys-apps/sdparm *** Package in world file is not installed: dev-python/mysql-python *** Package in world file is not installed: dev-util/kdevelop *** Package in world file is not installed: dev-util/kdbg *** Package in world file is not installed: sys-process/vixie-cron *** Package in world file is not installed: sys-apps/xinetd *** Package in world file is not installed: sys-process/anacron *** Package in world file is not installed: app-admin/apachetop *** Package in world file is not installed: sys-kernel/vanilla-sources *** Package in world file is not installed: sys-apps/iproute2 *** Package in world file is not installed: app-admin/gps *** Package in world file is not installed: app-editors/nano *** Package in world file is not installed: dev-util/ltrace *** Package in world file is not installed: dev-lang/gnat *** Package in world file is not installed: net-misc/ntp *** Package in world file is not installed: net-analyzer/nmap *** Package in world file is not installed: net-analyzer/snortsam *** Package in world file is not installed: dev-libs/elfutils *** Package in world file is not installed: sys-apps/x86info *** Package in world file is not installed: net-dns/dnsmasq *** Package in world file is not installed: dev-db/mysql-administrator *** Package in world file is not installed: dev-db/phpmyadmin *** Package in world file is not installed: app-editors/vim *** Package in world file is not installed: sys-apps/ivman *** Package in world file is not installed: mail-mta/postfix *** Package in world file is not installed: dev-lang/yasm *** Package in world file is not installed: net-dialup/rp-pppoe *** Package in world file is not installed: app-admin/logsentry *** Package in world file is not installed: dev-util/ccache *** Package in world file is not installed: dev-util/strace *** Package in world file is not installed: sys-apps/setserial !!! Invalid db entry: /var/db/pkg//sys-kernel !!! Invalid db entry: /var/db/pkg//dev-php !!! Invalid db entry: /var/db/pkg//x11-base !!! Invalid db entry: /var/db/pkg//x11-libs !!! Invalid db entry: /var/db/pkg//x11-misc !!! Invalid db entry: /var/db/pkg//www-client !!! Invalid db entry: /var/db/pkg//x11-terms !!! Invalid db entry: /var/db/pkg//app-admin !!! Invalid db entry: /var/db/pkg//app-crypt !!! Invalid db entry: /var/db/pkg//x11-themes !!! Invalid db entry: /var/db/pkg//perl-core !!! Invalid db entry: /var/db/pkg//gnome-base !!! Invalid db entry: /var/db/pkg//mail-mta !!! Invalid db entry: /var/db/pkg//app-arch !!! Invalid db entry: /var/db/pkg//app-i18n !!! Invalid db entry: /var/db/pkg//app-misc !!! Invalid db entry: /var/db/pkg//app-text !!! Invalid db entry: /var/db/pkg//sys-devel !!! Invalid db entry: /var/db/pkg//dev-db !!! Invalid db entry: /var/db/pkg//kde-base !!! Invalid db entry: /var/db/pkg//dev-dotnet !!! Invalid db entry: /var/db/pkg//media-gfx !!! Invalid db entry: /var/db/pkg//net-dns !!! Invalid db entry: /var/db/pkg//net-nds !!! Invalid db entry: /var/db/pkg//net-www !!! Invalid db entry: /var/db/pkg//media-libs !!! Invalid db entry: /var/db/pkg//sys-process !!! Invalid db entry: /var/db/pkg//sys-apps !!! Invalid db entry: /var/db/pkg//sys-libs !!! Invalid db entry: /var/db/pkg//net-fs !!! Invalid db entry: /var/db/pkg//net-libs !!! Invalid db entry: /var/db/pkg//net-mail !!! Invalid db entry: /var/db/pkg//net-misc !!! Invalid db entry: /var/db/pkg//net-print !!! Invalid db entry: /var/db/pkg//dev-java !!! Invalid db entry: /var/db/pkg//dev-lang !!! Invalid db entry: /var/db/pkg//dev-libs !!! Invalid db entry: /var/db/pkg//dev-perl !!! Invalid db entry: /var/db/pkg//dev-util !!! Invalid db entry: /var/db/pkg//dev-python !!! Invalid db entry: /var/db/pkg//app-editors !!! Invalid db entry: /var/db/pkg//sys-fs !!! Invalid db entry: /var/db/pkg//app-shells !!! Invalid db entry: /var/db/pkg//media-fonts !!! Invalid db entry: /var/db/pkg//media-sound !!! Invalid db entry: /var/db/pkg//gnome-extra !!! Invalid db entry: /var/db/pkg//app-doc !!! Invalid db entry: /var/db/pkg//net-analyzer *** Package in world file is not installed: /net-analyzer/ethereal *** Package in world file is not installed: kde-base/kdeaddons *** Package in world file is not installed: app-admin/logrotate *** Package in world file is not installed: app-crypt/gnupg *** Package in world file is not installed: net-analyzer/acid *** Package in world file is not installed: net-analyzer/oinkmaster *** Package in world file is not installed: kde-base/kdebase *** Package in world file is not installed: app-xemacs/ada *** Package in world file is not installed: sys-process/schedutils *** Package in world file is not installed: dev-php/jpgraph *** Package in world file is not installed: dev-util/oprofile *** Package in world file is not installed: kde-base/kdeadmin *** Package in world file is not installed: net-analyzer/traceroute *** Package in world file is not installed: dev-util/patchutils *** Package in world file is not installed: dev-util/git *** Package in world file is not installed: sys-boot/grub *** Package in world file is not installed: dev-util/ddd *** Package in world file is not installed: app-office/openoffice *** Package in world file is not installed: net-misc/whois *** Package in world file is not installed: sys-process/lsof *** Package in world file is not installed: sys-fs/sysfsutils *** Package in world file is not installed: sys-apps/coldplug *** Package in world file is not installed: www-client/mozilla-firefox *** Package in world file is not installed: net-www/mod_auth_mysql *** Package in world file is not installed: net-analyzer/iptraf *** Package in world file is not installed: net-dns/host *** Package in world file is not installed: kde-base/kde *** Package in world file is not installed: net-firewall/iptables *** Package in world file is not installed: app-portage/gentoolkit *** Package in world file is not installed: x11-libs/wxGTK *** Package in world file is not installed: dev-util/bitkeeper *** Package in world file is not installed: sys-apps/memtest86+ *** Package in world file is not installed: www-client/mozilla *** Package in world file is not installed: dev-db/mysqlnavigator *** Package in world file is not installed: net-analyzer/tcpdump *** Package in world file is not installed: dev-libs/dvmysql ...done! >>> Auto-cleaning packages ... >>> No outdated packages were found on your system. * GNU info directory index is up-to-date.
attach /var/lib/portage/world please
Created attachment 69778 [details, diff] Raise exception on invalid db entry Try giving this one a go too please. It applies to /usr/lib/portage/pym/portage.py.
Created attachment 69779 [details, diff] Prints information about the caller and how it was called Try this patch as well as the other one. The output from both should be useful.
Before doing any of the above, check /var/lib/portage/world for a line that begins with a "/". If you find one, remove the initial "/". Otherwise, proceed with the above.
Should be fixed in portage-2.0.53_rc3.
I am getting tons of "Invalid db entry" messages also. Should I open another bug? I have already updated to "sys-apps/portage-2.0.53_rc6" in hope of fixing this issue but things are unchanged. Here is my "emerge info" just in case: Portage 2.0.53_rc6 (default-linux/x86/2005.1, gcc-3.3.6, glibc-2.3.5-r3, 2.6.11-win4lin i686) ================================================================= System uname: 2.6.11-win4lin i686 AMD Athlon(tm) XP 2500+ Gentoo Base System version 1.6.13 distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [enabled] dev-lang/python: 2.3.5-r2, 2.4.2 sys-apps/sandbox: 1.2.12 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.15.92.0.2-r10 sys-devel/libtool: 1.5.20 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O3 -march=i686 -pipe -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-O3 -march=i686 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig buildpkg distcc distlocks fixpackages sandbox sfperms strict" GENTOO_MIRRORS="http://gentoo.ccccom.com http://gentoo.mirror.sdv.fr http://distro.ibiblio.org/pub/Linux/distributions/gentoo/ http://gentoo.mirrors.pair.com/ http://gentoo.osuosl.org/" MAKEOPTS="-j9" PKGDIR="/var/packages/" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage /usr/local/portage-fabrica" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 X a52 aac aalib alsa apm arts audiofile avi bitmap-fonts bzip2 bzlib cddb cdparanoia cdr crypt cups curl dga dts dvd edl eds emboss encode faac faad fam fame ffmpeg flac foomaticdb fortran gd gdbm gif gimpprint gmp gpm gstreamer gtk2 imagemagick imlib jbig jpeg jpeg2k junit kde kdeenablefinal lcms ldap libcaca libg++ libwww live lzo mad matroska md5sum mikmod mjpeg mng motif mp3 mpeg mysql ncurses nls ogg oggvorbis opengl oss pam pdflib perl png postgres ppds python qt quicktime readline real ruby samba scanner sdl speex spell ssl svg svga tcltk tcpd tga theora tiff truetype truetype-fonts type1-fonts udev unicode vcd vorbis win32codecs wmf xine xinerama xml2 xmms xv xvid xvmc zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS
You need to provide similar information; a sample of the exact messages you are getting, your world file, the traceback the patches give..
Open a new bug with that info though. It won't be fixed in 2.0.53 either way.
I reply to comment # 17 and comment # 18: It's there at bug # 110991.
