6

After an update of texlive 2011 (two days ago), biber (version 0.9.9) is completely broken. The solution found via google (deleting directory /tmp/par-.....) does not work. The Error is:

~/Git/DISS$ biber -h
Can't load '/tmp/par-6772656269/cache-   ab06f20732bfab23dfa35f56998ad4edca61bee1/608da891.so' 
for module XML::LibXML: /tmp/par-6772656269/cache-ab06f20732bfab23dfa35f56998ad4edca61bee1/libz.so.1: 
version `ZLIB_1.2.3.3' not found (required by /usr/lib/../lib/libxml2.so.2) at /usr/local/perl/lib/5.14.1/x86_64-linux-thread-multi/DynaLoader.pm line 190.
 at /usr/local/perl/lib/site_perl/5.14.1/PAR/Heavy.pm line 120
BEGIN failed--compilation aborted at XML/LibXML.pm line 153.
Compilation failed in require at XML/LibXML/Simple.pm line 16.
BEGIN failed--compilation aborted at XML/LibXML/Simple.pm line 16.
Compilation failed in require at Biber/LaTeX/Recode.pm line 9.
BEGIN failed--compilation aborted at Biber/LaTeX/Recode.pm line 9.
Compilation failed in require at Biber/Utils.pm line 21.
BEGIN failed--compilation aborted at Biber/Utils.pm line 21.
Compilation failed in require at Biber/Internals.pm line 8.
BEGIN failed--compilation aborted at Biber/Internals.pm line 8.
Compilation failed in require at (eval 22) line 2.
...propagated at /usr/local/perl/lib/5.14.1/base.pm line 94.
BEGIN failed--compilation aborted at Biber.pm line 5.
Compilation failed in require at script/biber line 20.
BEGIN failed--compilation aborted at script/biber line 20.

Any ideas how to get rid of that problem? I should finish my thesis instead of fighting biber errors ;-/

Thanks in advance!

Some further information after searching quite a while and texlive reinstallation: biber searches in /usr/local/perl/lib/5.14.1/ which does not exist anymore after update. Thus, the error is related to a debian update and not the texlive update.

The problem now is that I do not have a clue where biber gets that path from. If I know that I can adjust the path and it sould work. If it is "hardcoded" I will try to make a symbolic link tomorrow

louis cypher
  • 1,333
  • 2
    By the way, if you're finish your thesis, I strongly recommend you don't update TeX Live (or anything critical) on the machine you're using for that until your thesis is completed, unless you really know why you need the update (and even then, update only the specific package you need). Every update comes with a risk of breaking things. – mpg Apr 18 '12 at 11:09
  • 3
    Unless you really need version 0.9.9 of biber, you can downgrade it using tlmgr which makes backups before upgrades by default. Try tlmgr restore biber to see the list of revisions, then tlmgr restore biber <number> to restore to the given revision. – mpg Apr 18 '12 at 11:12
  • Thanks a lot. I called myself an idiot because I didn't make a backup. That is great news. As soon as I am back home I'll do that and freeze the system until submission of the thesis (I hoped to get an improved version of biblatex-chicago) – louis cypher Apr 18 '12 at 13:44
  • Sadly rolling back does not change anything. I guess it is related to my system update and not the new biber version =-( – louis cypher Apr 18 '12 at 19:11
  • The perl path you see is misleading - that is the path on the machine I built biber on. The binary version of biber needs no perl at all to run (it has its own internally. The issue is the zlib version for some reason. This is strange as biber should also contain its own, correct zlib version. The only libraries it uses from the OS are really fundamental ones like libc. I'll look into it a bit. – PLK Apr 19 '12 at 04:23
  • Thanks a lot for the information. That saves me a lot of effort – louis cypher Apr 19 '12 at 07:08
  • It looks like you are using the 64-bit biber for linux - you are, I assume on 64-bit debian? – PLK Apr 19 '12 at 07:33
  • 1
    Please can you try the binary here: http://sourceforge.net/projects/biblatex-biber/files/biblatex-biber/testfiles/biber-linux_x86_64.tar.gz

    I have changed the build procedure for linux to hopefully fix this.

     – PLK Apr 19 '12 at 09:46
  • yes it is debain 64-bit squeeze updated on 14th of april. – louis cypher Apr 19 '12 at 09:46
  • I'll give it a try as soon as I am back home. Thanks for the marvellous support. – louis cypher Apr 19 '12 at 09:48
  • Sadly no changes with that version – louis cypher Apr 19 '12 at 19:37
  • 2
    Could you open a bug on the biber SourceForge tracker? I think we need to move it to there to diagnose. This is very strange. – PLK Apr 19 '12 at 20:38
  • I'll do that as soon as I am at home. Best Markus – louis cypher Apr 20 '12 at 17:51
  • I have just booted a live CD of Debian Squeeze and I can run biber without any problem. What sort of update to the OS did you do? – PLK Apr 20 '12 at 20:37
  • it worked fine until I updated perl via 'apt-get update && apt-get upgrade'. BTW I opened a bug report on SF – louis cypher Apr 20 '12 at 21:43
  • 1
    For reference; The potential bug is tracked here https://sourceforge.net/tracker/?func=detail&aid=3519958&group_id=228270&atid=1073792 It could be a bug in Debians new Multiarch move. A temporary fix in Debian Sid is to create a symlink /usr/lib/libz.so.1 -> /usr/lib/x86_64-linux-gnu/libz.so.1 – Mikael Öhman Apr 22 '12 at 00:15

2 Answers2

3

This was a problem with some bad RPATHs hard-coded into some linux XML libraries which biber included. This meant that biber was using the OS libxml2 which it shouldn't have been doing. Wheezy has a very recent libxml2 which conflicted badly with the Perl XML::LibXML module. It's now fixed and shouldn't happen again in the future as the build process removes all RPATH settings from biber's own libraries (RPATH settings should never have been there in the first place). All binaries have been updated on SF.

PLK
  • 22,776
  • Do you know whether the version in texlive is updated also? I have some weird behaviour with the version you compiled for us. (some second occurances of a cite produce empty brackets). Or sould I rather pick the binary from SF? – louis cypher May 02 '12 at 19:34
  • texlive is not updated - it probably won't be until version 1.0 Can you open a ticket about the issue? That sounds like a normal bug/issue than anything to do with the binary per se - it sounds too specific. – PLK May 03 '12 at 12:45
  • I'll do after submitting my thesis. Is the new version different from the one you compile us/ is it worth updating? – louis cypher May 03 '12 at 21:25
  • Version 1.0 is for use only with biblatex 2.0+. both are beta so finish your thesis first ... – PLK May 04 '12 at 07:08
  • I was referring to the version with the fixed path, not the 1.0 beta. I love risk but I am not nuts ;-) – louis cypher May 04 '12 at 14:29
  • No, the one I compiled for you chaps is exactly the same as the one on SF. – PLK May 04 '12 at 17:18
2

This is similar to Engines of Tex-Editors and Biber/Biblatex, only the platform is different.

Do, from a shell,

rm -fr /tmp/par-6772656269

This should get rid of the precompiled libraries and create new ones.

However, this might be caused by a missing or misplaced zlib. Does the problem reappear after the rm -fr command?

Community
  • 1
egreg
  • 1,121,712
  • Yes it does. That was the solution I have been referring to. And it is the reason why I opened the question since it doesn't work =-( – louis cypher Apr 18 '12 at 13:26
  • On my Ubuntu 11.10 I have libz.so.1.2.3.4, but I don't know to what Debian it corresponds. Did you try updating libz? – egreg Apr 18 '12 at 14:00
  • I cannot find libz in the package manager. I installed everything that looks alike, such as lib32z1 without any change – louis cypher Apr 18 '12 at 19:10
  • The path /usr/local/perl/lib/ does not exist at all. It looks like something changed in the perl installation on debian... – louis cypher Apr 18 '12 at 19:29
  • I am pretty sure, that the path to the perl installation has changed due to upgrade of perl from 5.14.1 to 5.14.2. Perl is now under:/usr/local/lib/perl/5.14.2/ Sadly I do not have any idea where biber does get the path from... – louis cypher Apr 18 '12 at 19:58
  • Amazingly enough, for me the rm -rf trick worked :) (Ubuntu 11.04) - many thanks for noting it! Cheers! – sdaau Apr 29 '12 at 12:41