How to fix Yum when it hangs at “Setting up Package Sacks”

When installing Fedora 12 today (installing a new copy after troubles during the upgrade from Fedora 11), I got problems with yum, which tended to hang without any error message. I killed it (“kill” failed and I had to use “kill -9”, which worked), cleaned it (yum clean all), rebuilt the RPM database (I don’t even remember this command, sth like rpm -rebuild, and I found out later that this might be quite risky, apparently), manually deleted some RPM data files, and also ran my yum commands in verbose mode. All I could get was yum hanging at “Setting up Package Sacks”, or after what I thought was the end of downloading repository summaries. Anyway, I was just being impatient: after letting it run in the background for maybe 5 minutes, I got an error message saying that a repo (rpmfusion, which I used for VLC) timed out…

Could not retrieve mirrorlist http://mirrors.rpmfusion.org/mirrorlist?repo=free-fedora-12&arch=x86_64 error was
12: Timeout on http://mirrors.rpmfusion.org/mirrorlist?repo=free-fedora-12&arch=x86_64: (28, ”)
Error: Cannot retrieve repository metadata (repomd.xml) for repository: rpmfusion-free. Please verify its path and try again

The fix is simple: remove the faulty repo (what I did was I uninstalled the faulty repo and reinstalled a working copy – more precisely, I removed the repo manually from /etc/yum.repos.d/ then found out I should uninstall them properly with rpm -e rpmfusion-free-release-10-5.noarch). And to make sure this trap won’t ever catch me again, I dramatically decreased the timeout delay for yum, from the default 30 seconds to just 1: edit /etc/yum.conf and add timeout=1.

Other sources:
– how to remove repository?
– How to fix a yum when it hangs with no error messages

Bonus: a pretty long console log of me trying to install VLC, then messing with the rpm database and yum. I read somewhere that this rebuilding stuff is risky, so beware… yet my Fedora is fine now, despite all I did to hurt it! 🙂 Noobs like me may find useful commands, confirmed users will probably have some fun 😀 Note how miserably a the standard kills fail, while kill -9 is good.

[david@dodora12 ~]$ su
Password:
[root@dodora12 david]# rpm -ivh http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm
Retrieving http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm
warning: /var/tmp/rpm-tmp.vwxnDR: Header V3 DSA signature: NOKEY, key ID 49c8885a
Preparing… ########################################### [100%]
1:rpmfusion-free-release ########################################### [100%]
[root@dodora12 david]# yum install vlc
Loaded plugins: presto, refresh-packagekit
Existing lock /var/run/yum.pid: another copy is running as pid 2331.
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: PackageKit
Memory : 22 M RSS (317 MB VSZ)
Started: Sat Dec 19 18:21:01 2009 – 00:26 ago
State : Sleeping, pid: 2331
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: PackageKit
Memory : 22 M RSS (317 MB VSZ)
Started: Sat Dec 19 18:21:01 2009 – 00:28 ago
State : Sleeping, pid: 2331
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: PackageKit
Memory : 22 M RSS (317 MB VSZ)
Started: Sat Dec 19 18:21:01 2009 – 00:30 ago
State : Sleeping, pid: 2331
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: PackageKit
Memory : 22 M RSS (317 MB VSZ)
Started: Sat Dec 19 18:21:01 2009 – 00:32 ago
State : Sleeping, pid: 2331
^C

Exiting on user cancel.
[root@dodora12 david]# yum install vlc
Loaded plugins: presto, refresh-packagekit
Existing lock /var/run/yum.pid: another copy is running as pid 2331.
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: PackageKit
Memory : 22 M RSS (317 MB VSZ)
Started: Sat Dec 19 18:21:01 2009 – 00:47 ago
State : Sleeping, pid: 2331
^C

Exiting on user cancel.
[root@dodora12 david]# kill 2331
[root@dodora12 david]# kill 2331
bash: kill: (2331) – No such process
[root@dodora12 david]# yum install vlc
Loaded plugins: presto, refresh-packagekit
^C^Z
[1]+ Stopped yum install vlc
[root@dodora12 david]# yum install vlc -v
Not loading “blacklist” plugin, as it is disabled
Loading “presto” plugin
Loading “refresh-packagekit” plugin
Not loading “whiteout” plugin, as it is disabled
Config time: 0.057
Yum Version: 3.2.25
Existing lock /var/run/yum.pid: another copy is running as pid 2334.
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: yum
Memory : 22 M RSS (323 MB VSZ)
Started: Sat Dec 19 18:21:56 2009 – 00:25 ago
State : Traced/Stopped, pid: 2334
^C

Exiting on user cancel.
[root@dodora12 david]# kill 2334
[root@dodora12 david]#
[root@dodora12 david]# kill 2334
[root@dodora12 david]# kill -9 2334
[root@dodora12 david]# kill -9 2334
bash: kill: (2334) – No such process
[1]+ Killed yum install vlc
[root@dodora12 david]# yum install vlc -v
Not loading “blacklist” plugin, as it is disabled
Loading “presto” plugin
Loading “refresh-packagekit” plugin
Not loading “whiteout” plugin, as it is disabled
Config time: 0.065
Yum Version: 3.2.25
Setting up Package Sacks
^C^Z
[1]+ Stopped yum install vlc -v
[root@dodora12 david]# yum clean all
Loaded plugins: presto, refresh-packagekit
Existing lock /var/run/yum.pid: another copy is running as pid 2336.
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: yum
Memory : 22 M RSS (323 MB VSZ)
Started: Sat Dec 19 18:22:35 2009 – 00:13 ago
State : Traced/Stopped, pid: 2336
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: yum
Memory : 22 M RSS (323 MB VSZ)
Started: Sat Dec 19 18:22:35 2009 – 00:15 ago
State : Traced/Stopped, pid: 2336
^Z
[2]+ Stopped yum clean all
[root@dodora12 david]# kill -9 2336
[root@dodora12 david]# kill -9 2336
bash: kill: (2336) – No such process
[1]- Killed yum install vlc -v
[root@dodora12 david]# yum clean all
Loaded plugins: presto, refresh-packagekit
Cleaning up Everything
[root@dodora12 david]# yum install vlc
Loaded plugins: presto, refresh-packagekit
fedora/metalink | 28 kB 00:00
fedora | 4.2 kB 00:00
fedora/primary_db | 12 MB 00:11
^Z
[3]+ Stopped yum install vlc
[root@dodora12 david]# yum clean all
Loaded plugins: presto, refresh-packagekit
Existing lock /var/run/yum.pid: another copy is running as pid 2339.
Another app is currently holding the yum lock; waiting for it to exit…
The other application is: yum
Memory : 23 M RSS (326 MB VSZ)
Started: Sat Dec 19 18:23:02 2009 – 02:01 ago
State : Traced/Stopped, pid: 2339
^Z
[4]+ Stopped yum clean all
[root@dodora12 david]# kill -9 2339
[root@dodora12 david]# yum clean all
Loaded plugins: presto, refresh-packagekit
Cleaning up Everything
[3]- Killed yum install vlc
[root@dodora12 david]# cd /var/lib/rpm
[root@dodora12 rpm]# ls
Basenames __db.003 Installtid Provideversion Sigmd5
Conflictname __db.004 Name Pubkeys Triggername
__db.000 Dirnames Obsoletename Requirename
__db.001 Filedigests Packages Requireversion
__db.002 Group Providename Sha1header
[root@dodora12 rpm]# rm __db*
rm: remove regular empty file `__db.000′? y
rm: remove regular file `__db.001′? y
rm: remove regular file `__db.002′? y
rm: remove regular file `__db.003′? y
rm: remove regular file `__db.004′? y
[root@dodora12 rpm]# yum clean all
Loaded plugins: presto, refresh-packagekit
Cleaning up Everything
[root@dodora12 rpm]# yum clean all
Loaded plugins: presto, refresh-packagekit
Cleaning up Everything
[root@dodora12 rpm]# rpm –rebuilddb
[root@dodora12 rpm]# yum clean all
Loaded plugins: presto, refresh-packagekit
Cleaning up Everything
[root@dodora12 rpm]# yum update
Loaded plugins: presto, refresh-packagekit
fedora/metalink | 28 kB 00:00
fedora | 4.2 kB 00:00
fedora/primary_db | 12 MB 00:10
Could not retrieve mirrorlist http://mirrors.rpmfusion.org/mirrorlist?repo=free-fedora-12&arch=x86_64 error was
12: Timeout on http://mirrors.rpmfusion.org/mirrorlist?repo=free-fedora-12&arch=x86_64: (28, ”)
Error: Cannot retrieve repository metadata (repomd.xml) for repository: rpmfusion-free. Please verify its path and try again
[root@dodora12 rpm]#