Your message dated Tue, 01 Mar 2022 09:18:37 +0000
with message-id <e1noyet-0001yn...@fasolo.debian.org>
and subject line Bug#1006384: fixed in logol 1.7.9+dfsg-2
has caused the Debian Bug report #1006384,
regarding swi-prolog breaks logol autopkgtest: Program exited with wrong status
code
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.
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--
1006384: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006384
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: swi-prolog, logol
Control: found -1 swi-prolog/8.4.2+dfsg-2
Control: found -1 logol/1.7.9+dfsg-1
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of swi-prolog the autopkgtest of logol fails in
testing when that autopkgtest is run with the binary packages of
swi-prolog from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
swi-prolog from testing 8.4.2+dfsg-2
logol from testing 1.7.9+dfsg-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of swi-prolog to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=swi-prolog
https://ci.debian.net/data/autopkgtest/testing/amd64/l/logol/19529867/log.gz
calling logol with parameters -g 1799.logol -s 1799.fasta -dna
log4j:ERROR setFile(null,true) call failed.
java.io.FileNotFoundException: /var/log/logol/logol.log (Permission denied)
at java.base/java.io.FileOutputStream.open0(Native Method)
at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298)
at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:237)
at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:158)
at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)
at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)
at
org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)
at
org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)
at
org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)
at
org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)
at
org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
at
org.apache.log4j.PropertyConfigurator.parseCatsAndRenderers(PropertyConfigurator.java:672)
at
org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:516)
at
org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
at
org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
at org.apache.log4j.LogManager.<clinit>(LogManager.java:127)
at org.apache.log4j.Logger.getLogger(Logger.java:117)
at org.irisa.genouest.logol.Logol.<clinit>(Unknown Source)
For help, use option -h
INFO org.irisa.genouest.logol.Logol - Using configuration file:
/usr/share/logol/prolog/logol.properties
INFO org.irisa.genouest.logol.Logol - option g called with 1799.logol
INFO org.irisa.genouest.logol.Logol - option s called with 1799.fasta
INFO org.irisa.genouest.logol.Logol - No maximum solutions defined,
using defaults
INFO org.irisa.genouest.logol.Logol - option dna called
INFO org.irisa.genouest.logol.Logol - Start analyse to create grammar
analyser
Executing prolog for pre-analyse
java.io.FileNotFoundException:
/tmp/1799.logol.be129f0a-eeb3-4c10-a744-e5ccabb1087e.pre.res (No such
file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
at java.base/java.io.FileReader.<init>(FileReader.java:75)
at org.irisa.genouest.logol.Logol.loadVariables2Postpone(Unknown Source)
at org.irisa.genouest.logol.Logol.generatePreAnalysis(Unknown Source)
at org.irisa.genouest.logol.Logol.analyse(Unknown Source)
at org.irisa.genouest.logol.Logol.execute(Unknown Source)
at org.irisa.genouest.logol.Logol.main(Unknown Source)
INFO org.irisa.genouest.logol.Logol - Analyse in progress..
WARN org.irisa.genouest.logol.SequenceAnalyser - Path to suffix search
tool is not set in system environment. Will try to execute directly but
may fail if not in PATH of current user
ERROR org.irisa.genouest.logol.SequenceAnalyser - Program exited with
wrong status code: 134
Exception in thread "main" org.irisa.genouest.logol.GrammarException:
ERROR: Coudld not execute program: Program exited with wrong status code
at org.irisa.genouest.logol.Logol.execute(Unknown Source)
at org.irisa.genouest.logol.Logol.main(Unknown Source)
autopkgtest [10:27:07]: test run-unit-test
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: logol
Source-Version: 1.7.9+dfsg-2
Done: Olivier Sallou <osal...@debian.org>
We believe that the bug you reported is fixed in the latest version of
logol, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1006...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <osal...@debian.org> (supplier of updated logol package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 01 Mar 2022 08:54:23 +0000
Source: logol
Architecture: source
Version: 1.7.9+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Olivier Sallou <osal...@debian.org>
Closes: 1006384
Changes:
logol (1.7.9+dfsg-2) unstable; urgency=medium
.
* Source only upload, rebuilding against swi-prolog/8.4.2+dfsg-2 after
swi-prolog ABI break (Closes: #1006384).
Checksums-Sha1:
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256b486488528e71401089b7e81fdb9c5355fe7a 11123
logol_1.7.9+dfsg-2_source.buildinfo
Checksums-Sha256:
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Files:
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c95da5f4367a70fa5a70fbe8091486f5 12644 science optional
logol_1.7.9+dfsg-2.debian.tar.xz
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logol_1.7.9+dfsg-2_source.buildinfo
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