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Bug#977810: marked as done (biber: Fails with exit code 9 - panic: MUTEX_LOCK (22) [Magic.xs:525] during global destruction.)



Your message dated Wed, 23 Dec 2020 09:01:20 +0100
with message-id <[🔎] bd5b8108-c54e-de9c-24b1-b1e1a0d32caa@pa-w.de>
and subject line Re: Bug#977810: biber: Fails with exit code 9 - panic: MUTEX_LOCK (22) [Magic.xs:525] during global destruction.
has caused the Debian Bug report #977810,
regarding biber: Fails with exit code 9 - panic: MUTEX_LOCK (22) [Magic.xs:525] during global destruction.
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
977810: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=977810
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message ---
Package: biber
Version: 2.15-1
Severity: important
X-Debbugs-Cc: debian@pa-w.de

Dear Maintainer,

when running biber, it fails at properly destructing its objects,
leading to an exit code of 9 (and therefore, breaking any other programs
that call biber themselves).
This can be reproduced with arbitrary TeX and bibliography files. From a
minimal example:

$ biber example
INFO - This is Biber 2.15
INFO - Logfile is 'example.blg'
INFO - Reading 'example.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'bibliography.bib' for section 0
INFO - LaTeX decoding ...
INFO - Found BibTeX data source 'bibliography.bib'
INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
INFO - Sorting list 'nty/global//global/global' of type 'entry' with template 'nty' and locale 'en-US'
INFO - No sort tailoring available for locale 'en-US'
INFO - Writing 'example.bbl' with encoding 'UTF-8'
INFO - Output to example.bbl
panic: MUTEX_LOCK (22) [Magic.xs:525] during global destruction.
$ echo $?
9


Except for the non-zero return value and the panic message, it does work
as expected; i.e., the required output files are correctly created.
However, for example when compiling a TeX file, the latexmk process requires
multiple attempts as the first attempt is aborted due to the "failing" biber
call.


-- System Information:
Debian Release: bullseye/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 5.9.0-4-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages biber depends on:
ii  libautovivification-perl          0.18-1+b3
ii  libbusiness-isbn-perl             3.005-1
ii  libbusiness-ismn-perl             1.201-1
ii  libbusiness-issn-perl             1.004-1
ii  libclass-accessor-perl            0.51-1
ii  libdata-compare-perl              1.27-1
ii  libdata-dump-perl                 1.23-1
ii  libdata-uniqid-perl               0.12-1
ii  libdate-simple-perl               3.0300-3+b1
ii  libdatetime-calendar-julian-perl  0.102-1
ii  libdatetime-format-builder-perl   0.8300-1
ii  libdatetime-perl                  2:1.53-1
ii  libencode-eucjpms-perl            0.07-3+b9
ii  libencode-hanextra-perl           0.23-5+b3
ii  libencode-jis2k-perl              0.03-1+b7
ii  libfile-slurper-perl              0.012-1
ii  libipc-run3-perl                  0.048-2
ii  liblingua-translit-perl           0.28-1
ii  liblist-allutils-perl             0.18-1
ii  liblist-moreutils-perl            0.430-2
ii  liblog-log4perl-perl              1.53-1
ii  liblwp-protocol-https-perl        6.09-1
ii  libparse-recdescent-perl          1.967015+dfsg-2
ii  libreadonly-perl                  2.050-2
ii  libregexp-common-perl             2017060201-1
ii  libsort-key-perl                  1.33-2+b3
ii  libtext-bibtex-perl               0.88-3+b2
ii  libtext-csv-perl                  2.00-1
ii  libtext-csv-xs-perl               1.44-1+b1
ii  libtext-roman-perl                3.5-2
ii  libunicode-linebreak-perl         0.0.20190101-1+b3
ii  liburi-perl                       5.05-1
ii  libwww-perl                       6.49-1
ii  libxml-libxml-simple-perl         1.01-1
ii  libxml-libxslt-perl               1.99-1+b1
ii  libxml-writer-perl                0.900-1
ii  perl [libunicode-collate-perl]    5.32.0-6
ii  tex-common                        6.15

Versions of packages biber recommends:
ii  texlive-bibtex-extra  2020.20201129-1

biber suggests no packages.

-- no debconf information

--- End Message ---
--- Begin Message ---
Hi Norbert,

That leaves as explanation some environment variables, or other perl overrides that change the behaviour.

Thanks for this clue. I indeed had the following environment variable
(which fixed segfaults with some urxvt Perl plugins):

PERL_DESTRUCT_LEVEL=2

Unsetting this environment variable fixes the problem with biber.

Thanks again and sorry for the noise!

Best regards
Pascal

--- End Message ---

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