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Odd error when using python-updater [solved]
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evoweiss
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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
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Hu
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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?
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evoweiss
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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
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Hu
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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?
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evoweiss
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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
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tbart
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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..)
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tbart
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Joined: 31 Oct 2004
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Location: Baden // Austria

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)

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