Red Hat Bugzilla – Bug 1002494
yum crashes
Last modified: 2013-09-01 19:07:23 EDT
Description of problem: When installing or updating system, yum crashes and forces in most cases the system to reboot. I used the same machine (i7-3960X, 64 GB RAM, system on software raid) for more than one year now and until July, 20 it worked fine with different versions of Fedora and yum. A week ago I returned, made some "uge update" and then it didn't work anymore. Yum crashes when getting the file lists from the servers of the repositories via "/usr/bin/python /usr/libexec/urlgrabber-ext-down", ... etc. Usually I start the command "yum clean all && yum update -y -x emacs -x emacs-common" or just "yum clean all && yum update -y" since I added the line "exclude=emacs emacs-common" in my /etc/yum.conf. Strange enough, when stracing the whole procedure it goes through. I also tried to repair the rpmdb in /var/lib/rpm. Nothing worked. Today I've tried "strace -o /tmp/logbook yum provides "*/(libgphoto)"" and I've got (process:2224): GLib-WARNING **: GError set over the top of a previous GError or uninitialized memory. This indicates a bug in someone's code. You must ensure an error is NULL before it's set. The overwriting error message was: Parsing filelists.xml error: Start tag expected, '<' not found Traceback (most recent call last): File "/bin/yum", line 29, in <module> yummain.user_main(sys.argv[1:], exit_code=True) File "/usr/share/yum-cli/yummain.py", line 316, in user_main errcode = main(args) File "/usr/share/yum-cli/yummain.py", line 126, in main result, resultmsgs = base.doCommands() File "/usr/share/yum-cli/cli.py", line 532, in doCommands return self.yum_cli_commands[self.basecmd].doCommand(self, self.basecmd, self.extcmds) File "/usr/share/yum-cli/yumcommands.py", line 1503, in doCommand return base.provides(extcmds) File "/usr/share/yum-cli/cli.py", line 1516, in provides callback_has_matchfor=True) File "/usr/lib/python2.7/site-packages/yum/__init__.py", line 3324, in searchPackageProvides where = self.pkgSack.searchProvides(arg) File "/usr/lib/python2.7/site-packages/yum/packageSack.py", line 422, in searchProvides return self._computeAggregateListResult("searchProvides", name) File "/usr/lib/python2.7/site-packages/yum/packageSack.py", line 595, in _computeAggregateListResult sackResult = apply(method, args) File "/usr/lib/python2.7/site-packages/yum/sqlitesack.py", line 1404, in searchProvides ret = self.searchPrco(name, "provides") File "/usr/lib/python2.7/site-packages/yum/sqlitesack.py", line 46, in newFunc return func(*args, **kwargs) File "/usr/lib/python2.7/site-packages/yum/sqlitesack.py", line 1397, in searchPrco results.extend(self.searchFiles(n)) File "/usr/lib/python2.7/site-packages/yum/sqlitesack.py", line 46, in newFunc return func(*args, **kwargs) File "/usr/lib/python2.7/site-packages/yum/sqlitesack.py", line 934, in searchFiles self.populate(repo, mdtype='filelists') File "/usr/lib/python2.7/site-packages/yum/yumRepo.py", line 260, in populate dobj = repo_cache_function(xml, csum) File "/usr/lib64/python2.7/site-packages/sqlitecachec.py", line 54, in getFilelists self.repoid)) TypeError: Parsing filelists.xml error: Document is empty So this may be also a python problem. Version-Release number of selected component (if applicable): [root@bl4ckh0l3 ~]# rpm -qa | sort | grep -i yum PackageKit-yum-0.8.9-6.fc19.x86_64 PackageKit-yum-plugin-0.8.9-6.fc19.x86_64 yum-3.4.3-106.fc19.noarch yumex-3.0.10-2.fc19.noarch yum-langpacks-0.3.4-1.fc19.noarch yum-metadata-parser-1.1.4-8.fc19.x86_64 yum-utils-1.1.31-17.fc19.noarch
Created attachment 791695 [details] logbook
Thanks, this is probably helpfull. > stat("/var/cache/yum/x86_64/19/google-chrome/filelists.xml.gz", {st_mode=S_IFREG|0644, st_size=0, ...}) = 0 > getxattr("/var/cache/yum/x86_64/19/google-chrome/filelists.xml.gz", "user.yum.checksum.sha", "85349e796d9b7fd8421d086976731a17faf1a5fe", 40) = 40 This is it.. When yum verifies the file has correct checksum, it sets an xattr, so it does not have to calculate the checksum later. But here we see it's empty, but the checksum is set to the correct value. I feel there might be some FS issue.. didn't fsck complain recently? > stat("/var/cache/yum/x86_64/19/google-chrome/gen/filelists.xml", {st_mode=S_IFREG|0644, st_size=0, ...}) = 0 And the decompressed file is truncated, too.. but since both timestamps match, Yum does not bother decompressing, thus we don't compalin that filelists.xml.gz is not in gzip format, and crash later trying to parse the XML.. I think it might be worth adding a check/warn/unlink when we get correct cached checksum, but the file is empty. Anyway, just unlink /var/cache/yum/x86_64/19/google-chrome/filelists.xml.gz and this problem should go away.. but we still don't know the root cause (what has truncated it).
*** This bug has been marked as a duplicate of bug 920401 ***
Ahoi Jan & Zdeněk :-) My problem with yum is not really a yum/python problem. After several days of tracing the error I fond out that presumably a buggy version of xorg-x11-drv-nouveau forced my system to crash (submitted this to bug 1003314). Thnx anyway!