Description of problem: Today I ran the usual 'yum update' and yum aborted unexpectedly with several rpmdb errors, rendering rpmdb unusable. Version-Release number of selected component (if applicable): yum-3.0.1-2.fc6 rpm-4.4.2-32 kernel-2.6.18-1.2868.fc6 kernel-2.6.18-1.2869.fc6 How reproducible: Don't know how to reproduce the original conditions that caused the first yum traceback. Yum allways tracebacks from then now. Steps to Reproduce: 1. sudo yum update 2. 3. Actual results: Yum tracebacks Expected results: FC6 system updates normally Additional info: Here is the output of the first yum run: [tadej@tlinux-stable ~]$ sudo yum update Password: Loading "fastestmirror" plugin Loading "installonlyn" plugin Setting up Update Process Setting up repositories livna 100% |=========================| 1.1 kB 00:00 updates 100% |=========================| 1.2 kB 00:00 core 100% |=========================| 1.1 kB 00:00 macromedia 100% |=========================| 951 B 00:00 extras 100% |=========================| 1.1 kB 00:00 Determining fastest mirrors Reading repository metadata in from local files primary.xml.gz 100% |=========================| 105 kB 00:01 ################################################## 319/319 primary.xml.gz 100% |=========================| 405 kB 00:04 ################################################## 1088/1088 primary.xml.gz 100% |=========================| 1.7 MB 00:28 ################################################## 5459/5459 Resolving Dependencies --> Populating transaction set with selected packages. Please wait. ---> Downloading header for glibc-devel to pack into transaction set. glibc-devel-2.5-10.fc6.i3 100% |=========================| 105 kB 00:01 ---> Package glibc-devel.i386 0:2.5-10.fc6 set to be updated ---> Downloading header for libgcj-src to pack into transaction set. libgcj-src-4.1.1-51.fc6.i 100% |=========================| 48 kB 00:00 ---> Package libgcj-src.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for xterm to pack into transaction set. xterm-223-1.fc6.i386.rpm 100% |=========================| 11 kB 00:00 ---> Package xterm.i386 0:223-1.fc6 set to be updated ---> Downloading header for postgresql-libs to pack into transaction set. postgresql-libs-8.1.6-1.f 100% |=========================| 15 kB 00:00 ---> Package postgresql-libs.i386 0:8.1.6-1.fc6 set to be updated ---> Downloading header for glibc to pack into transaction set. glibc-2.5-10.fc6.i686.rpm 100% |=========================| 140 kB 00:01 ---> Package glibc.i686 0:2.5-10.fc6 set to be updated ---> Downloading header for xorg-x11-server-Xvfb to pack into transaction set. xorg-x11-server-Xvfb-1.1. 100% |=========================| 30 kB 00:00 ---> Package xorg-x11-server-Xvfb.i386 0:1.1.1-47.4.fc6 set to be updated ---> Downloading header for glib-devel to pack into transaction set. glib-devel-1.2.10-26.fc6. 100% |=========================| 7.7 kB 00:00 ---> Package glib-devel.i386 1:1.2.10-26.fc6 set to be updated ---> Downloading header for gimp-print-utils to pack into transaction set. gimp-print-utils-4.2.7-23 100% |=========================| 7.1 kB 00:00 ---> Package gimp-print-utils.i386 0:4.2.7-23.fc6 set to be updated ---> Downloading header for libstdc++ to pack into transaction set. libstdc++-4.1.1-51.fc6.i3 100% |=========================| 49 kB 00:00 ---> Package libstdc++.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for glibc-common to pack into transaction set. glibc-common-2.5-10.fc6.i 100% |=========================| 716 kB 00:08 ---> Package glibc-common.i386 0:2.5-10.fc6 set to be updated ---> Downloading header for autofs to pack into transaction set. autofs-5.0.1-0.rc3.2.i386 100% |=========================| 45 kB 00:00 ---> Package autofs.i386 1:5.0.1-0.rc3.2 set to be updated ---> Downloading header for dbus-devel to pack into transaction set. dbus-devel-1.0.1-9.fc6.i3 100% |=========================| 19 kB 00:00 ---> Package dbus-devel.i386 0:1.0.1-9.fc6 set to be updated ---> Downloading header for dbus to pack into transaction set. dbus-1.0.1-9.fc6.i386.rpm 100% |=========================| 21 kB 00:00 ---> Package dbus.i386 0:1.0.1-9.fc6 set to be updated ---> Downloading header for libgomp to pack into transaction set. libgomp-4.1.1-51.fc6.i386 100% |=========================| 49 kB 00:00 ---> Package libgomp.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for gcc-c++ to pack into transaction set. gcc-c++-4.1.1-51.fc6.i386 100% |=========================| 51 kB 00:00 ---> Package gcc-c++.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for cpuspeed to pack into transaction set. cpuspeed-1.2.1-1.43.fc6.i 100% |=========================| 7.5 kB 00:00 ---> Package cpuspeed.i386 1:1.2.1-1.43.fc6 set to be updated ---> Downloading header for wget to pack into transaction set. wget-1.10.2-8.fc6.1.i386. 100% |=========================| 17 kB 00:00 ---> Package wget.i386 0:1.10.2-8.fc6.1 set to be updated ---> Downloading header for libgcj to pack into transaction set. libgcj-4.1.1-51.fc6.i386. 100% |=========================| 56 kB 00:00 ---> Package libgcj.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for gcc-java to pack into transaction set. gcc-java-4.1.1-51.fc6.i38 100% |=========================| 51 kB 00:00 ---> Package gcc-java.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for gimp-print to pack into transaction set. gimp-print-4.2.7-23.fc6.i 100% |=========================| 26 kB 00:00 ---> Package gimp-print.i386 0:4.2.7-23.fc6 set to be updated ---> Downloading header for gcc-gfortran to pack into transaction set. gcc-gfortran-4.1.1-51.fc6 100% |=========================| 51 kB 00:00 ---> Package gcc-gfortran.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for wine-tools to pack into transaction set. wine-tools-0.9.29-1.fc6.i 100% |=========================| 20 kB 00:00 ---> Package wine-tools.i386 0:0.9.29-1.fc6 set to be updated ---> Downloading header for gimp-print-plugin to pack into transaction set. gimp-print-plugin-4.2.7-2 100% |=========================| 7.5 kB 00:00 ---> Package gimp-print-plugin.i386 0:4.2.7-23.fc6 set to be updated ---> Downloading header for krb5-libs to pack into transaction set. krb5-libs-1.5-13.i386.rpm 100% |=========================| 35 kB 00:00 ---> Package krb5-libs.i386 0:1.5-13 set to be updated ---> Downloading header for krb5-devel to pack into transaction set. krb5-devel-1.5-13.i386.rp 100% |=========================| 39 kB 00:00 ---> Package krb5-devel.i386 0:1.5-13 set to be updated ---> Downloading header for wine-core to pack into transaction set. wine-core-0.9.29-1.fc6.i3 100% |=========================| 66 kB 00:00 ---> Package wine-core.i386 0:0.9.29-1.fc6 set to be updated ---> Downloading header for dbus-x11 to pack into transaction set. dbus-x11-1.0.1-9.fc6.i386 100% |=========================| 17 kB 00:00 ---> Package dbus-x11.i386 0:1.0.1-9.fc6 set to be updated ---> Downloading header for glibc-headers to pack into transaction set. glibc-headers-2.5-10.fc6. 100% |=========================| 138 kB 00:01 ---> Package glibc-headers.i386 0:2.5-10.fc6 set to be updated ---> Downloading header for libgcj-devel to pack into transaction set. libgcj-devel-4.1.1-51.fc6 100% |=========================| 402 kB 00:05 ---> Package libgcj-devel.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for nscd to pack into transaction set. nscd-2.5-10.fc6.i386.rpm 100% |=========================| 100 kB 00:01 ---> Package nscd.i386 0:2.5-10.fc6 set to be updated ---> Downloading header for libstdc++-devel to pack into transaction set. libstdc++-devel-4.1.1-51. 100% |=========================| 129 kB 00:01 ---> Package libstdc++-devel.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for util-linux to pack into transaction set. util-linux-2.13-0.45.4.fc 100% |=========================| 64 kB 00:00 ---> Package util-linux.i386 0:2.13-0.45.4.fc6 set to be updated ---> Downloading header for shadow-utils to pack into transaction set. shadow-utils-4.0.17-11.fc 100% |=========================| 49 kB 00:00 ---> Package shadow-utils.i386 2:4.0.17-11.fc6 set to be updated ---> Downloading header for glib to pack into transaction set. glib-1.2.10-26.fc6.i386.r 100% |=========================| 8.1 kB 00:00 ---> Package glib.i386 1:1.2.10-26.fc6 set to be updated ---> Downloading header for setup to pack into transaction set. setup-2.6.1.1-1.fc6.noarc 100% |=========================| 18 kB 00:00 ---> Package setup.noarch 0:2.6.1.1-1.fc6 set to be updated ---> Downloading header for gcc-gnat to pack into transaction set. gcc-gnat-4.1.1-51.fc6.i38 100% |=========================| 207 kB 00:02 ---> Package gcc-gnat.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for lm_sensors to pack into transaction set. lm_sensors-2.10.1-1.fc6.i 100% |=========================| 26 kB 00:00 ---> Package lm_sensors.i386 0:2.10.1-1.fc6 set to be updated ---> Downloading header for libgfortran to pack into transaction set. libgfortran-4.1.1-51.fc6. 100% |=========================| 48 kB 00:00 ---> Package libgfortran.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for libgnat to pack into transaction set. libgnat-4.1.1-51.fc6.i386 100% |=========================| 48 kB 00:00 ---> Package libgnat.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for cpp to pack into transaction set. cpp-4.1.1-51.fc6.i386.rpm 100% |=========================| 52 kB 00:00 ---> Package cpp.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for libgcc to pack into transaction set. libgcc-4.1.1-51.fc6.i386. 100% |=========================| 49 kB 00:00 ---> Package libgcc.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for gcc to pack into transaction set. gcc-4.1.1-51.fc6.i386.rpm 100% |=========================| 59 kB 00:00 ---> Package gcc.i386 0:4.1.1-51.fc6 set to be updated ---> Downloading header for xorg-x11-server-Xorg to pack into transaction set. xorg-x11-server-Xorg-1.1. 100% |=========================| 42 kB 00:00 ---> Package xorg-x11-server-Xorg.i386 0:1.1.1-47.4.fc6 set to be updated --> Running transaction check Dependencies Resolved ============================================================================= Package Arch Version Repository Size ============================================================================= Updating: autofs i386 1:5.0.1-0.rc3.2 updates 766 k cpp i386 4.1.1-51.fc6 updates 2.6 M cpuspeed i386 1:1.2.1-1.43.fc6 updates 28 k dbus i386 1.0.1-9.fc6 updates 471 k dbus-devel i386 1.0.1-9.fc6 updates 38 k dbus-x11 i386 1.0.1-9.fc6 updates 28 k gcc i386 4.1.1-51.fc6 updates 4.9 M gcc-c++ i386 4.1.1-51.fc6 updates 3.3 M gcc-gfortran i386 4.1.1-51.fc6 updates 3.0 M gcc-gnat i386 4.1.1-51.fc6 updates 11 M gcc-java i386 4.1.1-51.fc6 updates 2.8 M gimp-print i386 4.2.7-23.fc6 updates 2.4 M gimp-print-plugin i386 4.2.7-23.fc6 updates 45 k gimp-print-utils i386 4.2.7-23.fc6 updates 22 k glib i386 1:1.2.10-26.fc6 extras 137 k glib-devel i386 1:1.2.10-26.fc6 extras 39 k glibc i686 2.5-10.fc6 updates 5.1 M glibc-common i386 2.5-10.fc6 updates 16 M glibc-devel i386 2.5-10.fc6 updates 2.0 M glibc-headers i386 2.5-10.fc6 updates 605 k krb5-devel i386 1.5-13 updates 1.7 M krb5-libs i386 1.5-13 updates 590 k libgcc i386 4.1.1-51.fc6 updates 81 k libgcj i386 4.1.1-51.fc6 updates 17 M libgcj-devel i386 4.1.1-51.fc6 updates 1.4 M libgcj-src i386 4.1.1-51.fc6 updates 11 M libgfortran i386 4.1.1-51.fc6 updates 218 k libgnat i386 4.1.1-51.fc6 updates 978 k libgomp i386 4.1.1-51.fc6 updates 69 k libstdc++ i386 4.1.1-51.fc6 updates 349 k libstdc++-devel i386 4.1.1-51.fc6 updates 9.4 M lm_sensors i386 2.10.1-1.fc6 updates 506 k nscd i386 2.5-10.fc6 updates 149 k postgresql-libs i386 8.1.6-1.fc6 updates 195 k setup noarch 2.6.1.1-1.fc6 updates 126 k shadow-utils i386 2:4.0.17-11.fc6 updates 1.0 M util-linux i386 2.13-0.45.4.fc6 updates 1.8 M wget i386 1.10.2-8.fc6.1 updates 581 k wine-core i386 0.9.29-1.fc6 extras 8.8 M wine-tools i386 0.9.29-1.fc6 extras 558 k xorg-x11-server-Xorg i386 1.1.1-47.4.fc6 updates 3.2 M xorg-x11-server-Xvfb i386 1.1.1-47.4.fc6 updates 1.6 M xterm i386 223-1.fc6 updates 324 k Transaction Summary ============================================================================= Install 0 Package(s) Update 43 Package(s) Remove 0 Package(s) Total download size: 117 M Is this ok [y/N]: y Downloading Packages: (1/43): glibc-devel-2.5-1 100% |=========================| 2.0 MB 00:27 (2/43): libgcj-src-4.1.1- 100% |=========================| 11 MB 02:37 (3/43): xterm-223-1.fc6.i 100% |=========================| 324 kB 00:03 (4/43): postgresql-libs-8 100% |=========================| 195 kB 00:01 (5/43): glibc-2.5-10.fc6. 100% |=========================| 5.1 MB 01:12 (6/43): xorg-x11-server-X 100% |=========================| 1.6 MB 00:15 (7/43): glib-devel-1.2.10 100% |=========================| 39 kB 00:00 (8/43): gimp-print-utils- 100% |=========================| 22 kB 00:00 (9/43): libstdc++-4.1.1-5 100% |=========================| 349 kB 00:03 (10/43): glibc-common-2.5 100% |=========================| 16 MB 02:58 (11/43): autofs-5.0.1-0.r 100% |=========================| 766 kB 00:07 (12/43): dbus-devel-1.0.1 100% |=========================| 38 kB 00:00 (13/43): dbus-1.0.1-9.fc6 100% |=========================| 471 kB 00:04 (14/43): libgomp-4.1.1-51 100% |=========================| 69 kB 00:00 (15/43): gcc-c++-4.1.1-51 100% |=========================| 3.3 MB 00:32 (16/43): cpuspeed-1.2.1-1 100% |=========================| 28 kB 00:00 (17/43): wget-1.10.2-8.fc 100% |=========================| 581 kB 00:05 (18/43): libgcj-4.1.1-51. 100% |=========================| 17 MB 03:08 (19/43): gcc-java-4.1.1-5 100% |=========================| 2.8 MB 00:41 (20/43): gimp-print-4.2.7 100% |=========================| 2.4 MB 00:24 (21/43): gcc-gfortran-4.1 100% |=========================| 3.0 MB 00:34 (22/43): wine-tools-0.9.2 100% |=========================| 558 kB 00:07 (23/43): gimp-print-plugi 100% |=========================| 45 kB 00:00 (24/43): krb5-libs-1.5-13 100% |=========================| 590 kB 00:07 (25/43): krb5-devel-1.5-1 100% |=========================| 1.7 MB 00:23 (26/43): wine-core-0.9.29 100% |=========================| 8.8 MB 02:24 (27/43): dbus-x11-1.0.1-9 100% |=========================| 28 kB 00:00 (28/43): glibc-headers-2. 100% |=========================| 605 kB 00:07 (29/43): libgcj-devel-4.1 100% |=========================| 1.4 MB 00:20 (30/43): nscd-2.5-10.fc6. 100% |=========================| 149 kB 00:01 (31/43): libstdc++-devel- 100% |=========================| 9.4 MB 02:07 (32/43): util-linux-2.13- 100% |=========================| 1.8 MB 00:26 (33/43): shadow-utils-4.0 100% |=========================| 1.0 MB 00:13 (34/43): glib-1.2.10-26.f 100% |=========================| 137 kB 00:01 (35/43): setup-2.6.1.1-1. 100% |=========================| 126 kB 00:01 (36/43): gcc-gnat-4.1.1-5 100% |=========================| 11 MB 02:29 (37/43): lm_sensors-2.10. 100% |=========================| 506 kB 00:06 (38/43): libgfortran-4.1. 100% |=========================| 218 kB 00:02 (39/43): libgnat-4.1.1-51 100% |=========================| 978 kB 00:12 (40/43): cpp-4.1.1-51.fc6 100% |=========================| 2.6 MB 00:35 (41/43): libgcc-4.1.1-51. 100% |=========================| 81 kB 00:00 (42/43): gcc-4.1.1-51.fc6 100% |=========================| 4.9 MB 01:09 (43/43): xorg-x11-server- 100% |=========================| 3.2 MB 00:46 rpmdb: /var/lib/rpm/Packages: page 1379: unpinned page returned rpmdb: PANIC: Invalid argument error: db4 error(-30977) from dbcursor->c_get: DB_RUNRECOVERY: Fatal error, run database recovery warning: rpmts_HdrFromFdno: Header V3 DSA signature: NOKEY, key ID 4f2a6fd2 rpmdb: PANIC: fatal region error detected; run recovery error: db4 error(-30977) from db->close: DB_RUNRECOVERY: Fatal error, run database recovery rpmdb: PANIC: fatal region error detected; run recovery error: db4 error(-30977) from db->close: DB_RUNRECOVERY: Fatal error, run database recovery rpmdb: PANIC: fatal region error detected; run recovery error: db4 error(-30977) from dbenv->close: DB_RUNRECOVERY: Fatal error, run database recovery rpmdb: PANIC: fatal region error detected; run recovery error: db4 error(-30977) from dbenv->open: DB_RUNRECOVERY: Fatal error, run database recovery error: cannot open Packages index using db3 - (-30977) error: cannot open Packages database in /var/lib/rpm Traceback (most recent call last): File "/usr/bin/yum", line 29, in ? yummain.main(sys.argv[1:]) File "/usr/share/yum-cli/yummain.py", line 180, in main base.doTransaction() File "/usr/share/yum-cli/cli.py", line 407, in doTransaction if self.gpgsigcheck(downloadpkgs) != 0: File "/usr/share/yum-cli/cli.py", line 486, in gpgsigcheck self.getKeyForPackage(po, lambda x, y, z: self.userconfirm()) File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 2003, in getKeyForPackage if misc.keyInstalled(ts, keyid, timestamp) >= 0: File "/usr/lib/python2.4/site-packages/yum/misc.py", line 253, in keyInstalled for hdr in ts.dbMatch('name', 'gpg-pubkey'): TypeError: rpmdb open failed Subsequent yum run output: [tadej@tlinux-stable ~]$ sudo yum update kernel Password: Loading "fastestmirror" plugin Loading "installonlyn" plugin rpmdb: PANIC: fatal region error detected; run recovery error: db4 error(-30977) from dbenv->open: DB_RUNRECOVERY: Fatal error, run database recovery error: cannot open Packages index using db3 - (-30977) error: cannot open Packages database in /var/lib/rpm Traceback (most recent call last): File "/usr/bin/yum", line 29, in ? yummain.main(sys.argv[1:]) File "/usr/share/yum-cli/yummain.py", line 85, in main base.getOptionsConfig(args) File "/usr/share/yum-cli/cli.py", line 199, in getOptionsConfig errorlevel=opts.errorlevel) File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 125, in doConfigSetup self.conf = config.readMainConfig(startupconf) File "/usr/lib/python2.4/site-packages/yum/config.py", line 597, in readMainConfig yumvars['releasever'] = _getsysver(startupconf.installroot, startupconf.distroverpkg) File "/usr/lib/python2.4/site-packages/yum/config.py", line 656, in _getsysver idx = ts.dbMatch('provides', distroverpkg) TypeError: rpmdb open failed This is really annoying, as it is a quite tedious task to recover rpmdb manually.
*** This bug has been marked as a duplicate of 213963 ***