Red Hat Bugzilla – Bug 109913
rpm segfaults, corrupts Packages db, cannot recover!
Last modified: 2007-11-30 17:10:33 EST
From Bugzilla Helper: User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031030 Description of problem: RPM segfaults while installing a package, and corrupts the "Packages" database. From that point on, rpm seems to be permanently messed up, with no obvious way to recover. Running any rpm command, including rpm --rebuilddb hangs, and it must be killed with -9. For instance: # rpm -v -v --rebuilddb D: rebuilding database /var/lib/rpm into /var/lib/rpmrebuilddb.2274 D: creating directory /var/lib/rpmrebuilddb.2274 D: opening old database with dbapi 3 D: opening db environment /var/lib/rpm/Packages joinenv D: opening db index /var/lib/rpm/Packages rdonly mode=0x0 (and it dies here.) Version-Release number of selected component (if applicable): rpm-4.2.1 How reproducible: Sometimes Steps to Reproduce: 1. Install Fedora Core (the "Everything" install) and then install a bunch of other RPMs (from FreshRPMs.net or whatever.) 2. Eventually rpm will segfault while installing an RPM and corrupt it's database. 3. Future rpm commands hang. Actual Results: rpm hangs after opening the Packages database. If I "mv /var/lib/rpm/Packages /var/lib/rpm/Packages.corrupt" then rpm --rebuilddb works, but doesn't actually rebuild the database. It produces a new Packages file which is only about 12K (the corrupted Packages file was over 50 MB) Expected Results: 1. rpm should NOT segfault when installing any RPM. 2. rpm should NOT corrupt it's database. 3. rpm --rebuilddb should actually rebuild the database, instead of doing whatever useless thing it actually did. 4. rpm should probably keep backup copies of it's databases around, so it can recover better from these catastrophic corruption problems. Additional info: I'd really like to know how to fix this problem without having to reinstall Fedora!
See http://www.rpm.org/hintskinks/repairdb/ which includes instructions on how to fix the Packages file. But first it might be worth trying rpm --rebuilddb on your original Packages file when the __db* files are removed (if you haven't already tried this).
rpm --import does not look too happy, either. # rpm -q rpm rpm-4.2.1-0.30.1 # rpm -q beecrypt beecrypt-3.0.1-0.20030630.1 # rpm -qf /lib/libc.so.6 glibc-2.3.2-4.80.8 # rpm -qa gpg-pubkey* # gpg /tmp/fedo.txt pub 1024D/4F2A6FD2 2003-10-27 Fedora Project <fedora@redhat.com> sub 1024g/FB939E34 2003-10-27 # rpm --import /tmp/fedo.txt # rpm -qa gpg-pubkey* error: rpmdbNextIterator: skipping h# 761 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 473 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 664 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 282 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 474 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 663 Header V3 DSA signature: BAD, key ID db42a60e gpg-pubkey-db42a60e-3f9d9db6 # rpm -qf /lib/libc.so.6 error: rpmdbNextIterator: skipping h# 663 Header V3 DSA signature: BAD, key ID db42a60e # rpm -qi gpg-pubkey-db42a60e-3f9d9db6 Name : gpg-pubkey Relocations: (not relocateable) Version : db42a60e Vendor: (none) Release : 3f9d9db6 Build Date: Wed Nov 19 03:09:56 2003 Install Date: Wed Nov 19 03:09:56 2003 Build Host: localhost Group : Public Keys Source RPM: (none) Size : 0 License: pubkey Signature : (none) Summary : gpg(Fedora Project <fedora@redhat.com>) Description : -----BEGIN PGP PUBLIC KEY BLOCK----- Version: rpm-4.2.1 (beecrypt-3.0.0) mQGiBD+dnTsRBACwnlz4AhctOLlVBAsq+RaU82nb5P3bD1YJJpsAce1Ckd2sBUOJD11NUCqH 8c7EctOquOZ5zTcWxHiWWbLyKQwUw2SUvnWa5SSbi8kI8q9MTPsPvhwtgMrQMLenMO+nsrxr SaG6XcD+ssfJNxC7NQVCQAj3pvvg9rKi3ygsM7CXHwCghgsqX6TOr55HE90DbEsoq3b/jjsD /i8aIZ6urUgrpAkQslcakXdJLKgSdwjRUgVZgvYZb7kAx1iPq0t/AhB3NJw3zW4AAKJohGg3 xj5K4V8PJEZrSIpoRYlF43Kqlfu2p5ghWT89SP4YAlWPeTqf0+dTYUYz3b144k2ZFOdRuXIR xunoYNAUr9oMrxBXbJ/eY+0UQX3pBACYzKizyY4JJgd0zFJmNkcdK9nzcm+btYFnYQo33w5G SE686UNr+9yiXt9tmPRvNEbj3u+xoAX8B/5k3aZ5NbUhV64/VcKlUdRIxNlFCG7I9KgxeHWA Ywi7yqOGXM3T/v6o7GLdQEB0ChFqS7kUlqmwLV+C3QhlrFe/Cuk26i+Q6rQiRmVkb3JhIFBy b2plY3QgPGZlZG9yYUByZWRoYXQuY29tPohGBBARAgAGBQI/ntjgAAoJECnVuiSN9W0FUSUA oJnrone4J0o1HMkRz+6g9KVuO2FyAJ0XyebOzVmI9U5OyOfnNmYV0wnQcohGBBMRAgAGBQI/ nZ22AAoJECGRgM3bQqYOR5QAoIp1G+omVktq/snxpmz5UeHjlSYjAKCRr/ea/L7S7ZTxB18c f1TYfad1x4hbBBMRAgAbBQI/nZ07BgsJCAcDAgMVAgMDFgIBAh4BAheAAAoJELRCadBPKm/S 2PAAnRTlhorITphab+oxAHtbxZF9BVyDAJ9WOVaZUG53IWWIAXOGv3j/cmr3lrkBDQQ/nZ08 EAQAugOfLWJbKwMA9vg2mJU594TZU0HRJkx/fqYhx0YxWWRpzplrEyvcDXuYcWi1Hwh0tD86 T4fR5GV6joWiWClzD+Hwhhb6gcSdeSGlGLlZAvWYtFSHWiv+3LaI9w8Vtczl99Bh2WiMDNDD Gw0RQg6ZaftldLSe4j1pffpFGQ8SuisAAwUEAKVxqLT7fC5xQ6oclcZ+PhoDlePQ1BiTS7tu GM07bFF4nNvY91LL7S31pooz3XbGSWP8jxzSv1Fw35YhSmWGOBOEXluqMbVQGJJ5m8fqJOjC 0imbfeWgr/T7zLrJeiljDxvX+6TyawyWQngF6v1Hq6FRV0O0bOp9Npt5zqCbDGs/iEYEGBEC AAYFAj+dnTwACgkQtEJp0E8qb9L//gCcDVYnDegNCOxDn1sedDwxw+0h8OcAn1CZHof15Qqx nTwEnvwF2QeOI5dn =7hyK -----END PGP PUBLIC KEY BLOCK----- I have older RH, not all-Fedora...
Try removing (or renaming) the /var/lib/rpm/Pubkeys index, and then doing rpm --rebuilddb -vv. This is essentially the same as adding --nosignature the hard way. Then repeat "rpm -qa" to see if segfault is fixed.
did you notice that comment was added by other guy than Torrey Hoffman... I am not having segfaults, "only" database corruption. # rpm -qa gpg-pubkey* # rpm --import /tmp/4F2A6FD2.txt # rpm -qa gpg-pubkey* error: rpmdbNextIterator: skipping h# 192 Header V3 DSA signature: BAD, key ID db42a60e gpg-pubkey-db42a60e-3f9d9db6 error: rpmdbNextIterator: skipping h# 553 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 457 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 311 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 503 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 191 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 388 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 533 Header V3 DSA signature: BAD, key ID db42a60e error: rpmdbNextIterator: skipping h# 357 Header V3 DSA signature: BAD, key ID db42a60e # rpm --checksig glibc-2.3.2-4.80.i686.rpm glibc-2.3.2-4.80.i686.rpm: (SHA1) DSA sha1 md5 GPG NOT OK but rm -f /var/lib/rpm/Pubkeys && rpm --rebuilddb -vv did not make any difference, so I'll just replace these broken database files from backup I made ten mins ago and ignore every signature verification failure and hope packages are not being tampered with. # sha1 glibc-2.3.2-4.80.i686.rpm SHA1(glibc-2.3.2-4.80.i686.rpm)= cf8b3b3a67bf8a011f083177fe081389f4590988
I have a similar case where removing the Pubkeys file and rebuilding rpmdb was a solution. My feeling is that it seems to be caused by importing keys and it might has something to do with apt-get.