"yum clean" hangs - what to try next?

linux yum strace

30,535

Solution 1

I had the same problem, all my yum commands were hanging.

I ran the following commands

rm /var/lib/rpm/__db*
rm /var/lib/rpm/.rpm.lock
rm /var/lib/rpm/.dbenv.lock

So a combination of some of the above comments and answers.

Solution 2

On my Redhat 7.2 this helps to let run the yum commands.

 rm /var/lib/rpm/.dbenv.lock

Solution 3

In my case, I had all but one server with

[main]
enabled=1

/etc/yum/pluginconf.d/subscription-manager.conf

Setting this to enabled=0 fixed my issue.

Solution 4

This is not a direct answer, but if none of the commands from the other answers helped then I'd check the command package-cleanup.

All the proposed commands are for handling the RPM database, but it could be that there's something broken in the relation of some installed packages.

From man package-cleanup:

DESCRIPTION
       package-cleanup is a program for cleaning up the locally-installed RPMs.
EXAMPLES
       List all dependency problems:
              package-cleanup --problems

       List all packages that are not in any Yum repository:
              package-cleanup --orphans

I'd start with the command in the second example, I've used it before and it solved some weird issues I had in one of my CentOS machines which was related to yum clean.

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30,535

Hamish Downer

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Updated on September 18, 2022

Comments

Hamish Downer over 1 year
I run a number of CentOS servers. I was recently doing the occasional yum update but this failed on a handful of the servers. On most I have been able to move forward by doing:
```
# yum clean all
# rm -f /var/lib/rpm/__db*
# rpm --rebuilddb
# yum update
```
However on one server, the yum clean command hangs. I have tried running:
```
# yum -v --noplugins clean all
```
but I get no output at all. Yum just hangs, and will sit there for hours if I let it, not using any cpu, just stopped. Doing
```
# strace -f yum -v --noplugins clean all
```
produces quite a lot of output, but then stops with:
```
...
stat64("/var/lib/rpm/__db.003", {st_mode=S_IFREG|0644, st_size=450560, ...}) = 0
open("/var/lib/rpm/__db.003", O_RDWR|O_LARGEFILE) = 4
fcntl64(4, F_SETFD, FD_CLOEXEC)         = 0
mmap2(NULL, 450560, PROT_READ|PROT_WRITE, MAP_SHARED, 4, 0) = 0xb6b34000
close(4)                                = 0
stat64("/var/lib/rpm/Packages", {st_mode=S_IFREG|0644, st_size=14938112, ...}) = 0
open("/var/lib/rpm/Packages", O_RDONLY|O_LARGEFILE) = 4
fcntl64(4, F_SETFD, FD_CLOEXEC)         = 0
read(4, "\0\0\0\0\1\0\0\0\0\0\0\0a\25\6\0\10\0\0\0\0\20\0\0\0\10\0\0k\t\0\0"..., 512) = 5
12
close(4)                                = 0
open("/var/lib/rpm/Packages", O_RDONLY|O_LARGEFILE) = 4
fcntl64(4, F_SETFD, FD_CLOEXEC)         = 0
fstat64(4, {st_mode=S_IFREG|0644, st_size=14938112, ...}) = 0
futex(0xb6b7bd1c, FUTEX_WAIT, 1, NULL
```
At this point I'm feeling stuck. This is a production server, so I don't want to just blow it away, or even blow away all the yum information. Apart from the yum stuff, the server is working fine.
- gokva about 12 years
  
  do you have any nfs mounted filesystems that are currently hung?
- Janne Pikkarainen about 12 years
  
  What does lsof reveal, if anything?
- Hamish Downer about 12 years
  
  There is a single root fs (with plenty of space) and then just proc, sysfs and tmpfs (and tmpfs has plenty of space).
- Hamish Downer about 12 years
  
  @JannePikkarainen - lsof /var/lib/rpm/Packages originally showed an old rpm process. I've killed that, and my yum, checked that lsof didn't show anything else accessing the file, and tried again, but I stop at the same place. I've also scanned through the full lsof output and not seen anything that looks likely.
- Hamish Downer about 12 years
  
  Also, I can open the file /var/lib/rpm/Packages for reading in another application.
- Janne Pikkarainen about 12 years
  
  Does the server have access to outside world? Yes, I know, yum is not supposed to contact the net that soon, but ...
- Hamish Downer about 12 years
  
  @JannePikkarainen - yes there is network access. I can ssh into and out of it, and ping other servers. I can load web pages in lynx.
- GioMac almost 12 years
  
  need output: rpm -qa|grep yum
- Brian almost 9 years
  
  Try doing the yum clean all along with yum update after rebuilding the databases (rm -f /var/lib/rpm/__db* and rpm --rebuilddb) instead of before.
dimiguel about 5 years

This corrupted my yum installation, but then running sudo rpm --rebuilddb && yum clean all did the trick.
David Morton almost 5 years

Brilliant! This worked like a charm for me! I saw the other superuser thread regarding a similar issue, but it turns out the locks were what were freezing it for me. Appreciate this greatly! superuser.com/questions/384963/yum-hangs-and-wont-respond
Lkbhai Lr about 3 years

second command helped me in centos