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evoweiss Veteran
Joined: 07 Sep 2003 Posts: 1678 Location: Edinburgh, UK
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Posted: Thu Dec 06, 2012 4:57 pm Post subject: Odd error when using python-updater [solved] |
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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
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* 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.
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Last edited by evoweiss on Fri Dec 07, 2012 7:25 am; edited 1 time in total |
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Hu Moderator
Joined: 06 Mar 2007 Posts: 21633
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Posted: Thu Dec 06, 2012 10:51 pm Post subject: |
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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? |
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evoweiss Veteran
Joined: 07 Sep 2003 Posts: 1678 Location: Edinburgh, UK
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Posted: Fri Dec 07, 2012 12:09 am Post subject: |
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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:
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# 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
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and
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# 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
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Best,
Alex |
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Hu Moderator
Joined: 06 Mar 2007 Posts: 21633
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Posted: Fri Dec 07, 2012 12:15 am Post subject: |
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That is definitely wrong. Have you previously experienced filesystem corruption or unclean shutdowns? Does it help to remove and reinstall that package? |
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evoweiss Veteran
Joined: 07 Sep 2003 Posts: 1678 Location: Edinburgh, UK
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Posted: Fri Dec 07, 2012 12:26 am Post subject: |
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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 |
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tbart Apprentice
Joined: 31 Oct 2004 Posts: 151
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Posted: Thu Apr 18, 2013 12:19 pm Post subject: |
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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..) |
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tbart Apprentice
Joined: 31 Oct 2004 Posts: 151
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Posted: Thu Apr 18, 2013 12:46 pm Post subject: |
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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
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Code: | emerge -1av $(find /var/db/pkg/ -name "*.bz2" -size 0 | atomgrep) |
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