Gentoo Forums
Gentoo Forums
Gentoo Forums
Quick Search: in
Odd error when using python-updater [solved]
View unanswered posts
View posts from last 24 hours

 
Reply to topic    Gentoo Forums Forum Index Portage & Programming
View previous topic :: View next topic  
Author Message
evoweiss
Veteran
Veteran


Joined: 07 Sep 2003
Posts: 1678
Location: Edinburgh, UK

PostPosted: Thu Dec 06, 2012 4:57 pm    Post subject: Odd error when using python-updater [solved] Reply with quote

Hi all,

I recently ran python-updater after upgrading to 3.2. I encountered the following error, which persists even after I've manually emerged the files. I tried fixing the bzip2 files. A check of dmesg did not indicate any problems with the HDD. Any ideas on how to deal with this would be appreciated.

Best,

Alex

Code:

* Starting Python Updater...
 * Main active version of Python:    3.2
 * Active version of Python 2:       2.7
 * Active version of Python 3:       3.2
 * Globally supported Python ABIs in installed repositories:
 *   gentoo:                         2.4 2.5 2.6 2.7 3.1 3.2 3.3 2.5-jython 2.7-pypy-1.7 2.7-pypy-1.8 2.7-pypy-1.9
 *   x-portage:                      2.4 2.5 2.6 2.7 3.1 3.2 3.3 2.5-jython 2.7-pypy-1.7 2.7-pypy-1.8 2.7-pypy-1.9
 *   Adding to list: dev-libs/boost:0
 *   Adding to list: dev-libs/libgamin:0
 *   Adding to list: dev-libs/libxslt:0
 *   Adding to list: dev-vcs/subversion:0
 *   Adding to list: media-libs/lcms:0
 *   Adding to list: sys-apps/file:0
 *   Adding to list: sys-devel/gdb:0
 *   Adding to list: sys-libs/cracklib:0

bzip2: Compressed file ends unexpectedly;
        perhaps it is corrupted?  *Possible* reason follows.
bzip2: Success
        Input file = /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2, output file = (stdout)

It is possible that the compressed file(s) have become corrupted.
You can use the -tvv option to test integrity of such files.

You can use the `bzip2recover' program to attempt to recover
data from undamaged sections of corrupted files.


bzip2: Compressed file ends unexpectedly;
        perhaps it is corrupted?  *Possible* reason follows.
bzip2: Success
        Input file = /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2, output file = (stdout)

It is possible that the compressed file(s) have become corrupted.
You can use the -tvv option to test integrity of such files.

You can use the `bzip2recover' program to attempt to recover
data from undamaged sections of corrupted files.

 * Missing metadata in '/var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2' file. Manually reinstall corresponding package.


Last edited by evoweiss on Fri Dec 07, 2012 7:25 am; edited 1 time in total
Back to top
View user's profile Send private message
Hu
Moderator
Moderator


Joined: 06 Mar 2007
Posts: 21490

PostPosted: Thu Dec 06, 2012 10:51 pm    Post subject: Reply with quote

Does bzip2 encounter problems accessing that file by hand? If yes, what is the output of file /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2 ; ls -l /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2?
Back to top
View user's profile Send private message
evoweiss
Veteran
Veteran


Joined: 07 Sep 2003
Posts: 1678
Location: Edinburgh, UK

PostPosted: Fri Dec 07, 2012 12:09 am    Post subject: Reply with quote

Hi,

Hu wrote:
Does bzip2 encounter problems accessing that file by hand? If yes, what is the output of file /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2 ; ls -l /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2?


Thanks for getting in touch. The results are as follows:

Code:

# file /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2
/var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2: empty


and

Code:

# ls -l /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2
-rw-r--r-- 1 root root 0 Sep 27 01:53 /var/db/pkg/virtual/perl-File-Temp-0.220.0-r2/environment.bz2


Best,

Alex
Back to top
View user's profile Send private message
Hu
Moderator
Moderator


Joined: 06 Mar 2007
Posts: 21490

PostPosted: Fri Dec 07, 2012 12:15 am    Post subject: Reply with quote

That is definitely wrong. Have you previously experienced filesystem corruption or unclean shutdowns? Does it help to remove and reinstall that package?
Back to top
View user's profile Send private message
evoweiss
Veteran
Veteran


Joined: 07 Sep 2003
Posts: 1678
Location: Edinburgh, UK

PostPosted: Fri Dec 07, 2012 12:26 am    Post subject: Reply with quote

Hu wrote:
That is definitely wrong. Have you previously experienced filesystem corruption or unclean shutdowns? Does it help to remove and reinstall that package?


I removed the file and reinstalled it. The file now is not blank. Hopefully that will have done the trick. I will report back later one way or another.

Update... that did the trick. Thanks.

Best,

Alex
Back to top
View user's profile Send private message
tbart
Apprentice
Apprentice


Joined: 31 Oct 2004
Posts: 151

PostPosted: Thu Apr 18, 2013 12:19 pm    Post subject: Reply with quote

Just wanted to chime in.
This happened to me as well during today's emerge -Dunv world.


no unclean shutdowns or fs corruption.

might have been caused by this: (in dmesg)
Code:
bzip2[9162]: segfault at 7f9471353018 ip 000000000040a13d sp 00007f9471b52e20 error 4 in pbzip2[400000+15000]


but I don't think repeated corruptions can stem from one segfault...

wait, there's more... no segfault, but:
Code:
pbzip2: *ERROR: File [/var/db/pkg/dev-libs/eio-1.7.6/environment.bz2] is NOT a valid bzip2!  Skipping...
-------------------------------------------
!!! FAILED prerm: 1
*** glibc detected *** bzip2: double free or corruption (out): 0x00007f2b729d6190 ***


I
Code:
quickpkg pbzip2 && emerge -C pbzip2
now, and it seems to work. Seems like pbzip2 is not that stable yet...

(Most likely not the evoweiss's problem, but I thought people might land here because of this bug as well..)
Back to top
View user's profile Send private message
tbart
Apprentice
Apprentice


Joined: 31 Oct 2004
Posts: 151

PostPosted: Thu Apr 18, 2013 12:46 pm    Post subject: Reply with quote

btw, this might come in handy:

Code:
cat /usr/local/bin/atomgrep
#!/bin/bash
[[ -n $1 && ! -f $1 ]] && { echo "Not a file, \"$1\". Provide a file to grep in or feed me stdin."; exit; }

sed -ne 's#.*\(\(\(\<\w\{2,6\}\>-\w*\)\|virtual\)\/\([a-zA-Z0-9+_]*\(-[^0-9]\w*\)*\)*\).*#\1#gp' $1


Code:
emerge -1av $(find /var/db/pkg/ -name "*.bz2" -size 0 | atomgrep)
Back to top
View user's profile Send private message
Display posts from previous:   
Reply to topic    Gentoo Forums Forum Index Portage & Programming All times are GMT
Page 1 of 1

 
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum