[Debian-med-packaging] Bug#1026056: swi-prolog breaks logol autopkgtest: Program exited with wrong status code

[olivier sallou]

Tests need to be run as root, or use a specific config file and use non
root writable directories.

Will try to change tests to do so.

Regarding issue itself,  programs compiled by swi prolog usually require
recompilation on swi prolog updates.

Will try to rebuild and check

Le mar. 13 déc. 2022, 22:03, Paul Gevers <elbrus at debian.org> a écrit :

> Source: swi-prolog, logol
> Control: found -1 swi-prolog/9.0.2+dfsg-1
> Control: found -1 logol/1.7.9+dfsg-5
> Severity: serious
> Tags: sid bookworm
> User: debian-ci at 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    9.0.2+dfsg-1
> logol                  from testing    1.7.9+dfsg-5
> all others             from testing    from testing
>
> I copied some of the output at the bottom of this report. The issue
> *looks* similar to bug 1022253, but now on all architectures.
>
> 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/29303003/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:293)
>         at java.base/java.io
> .FileOutputStream.<init>(FileOutputStream.java:235)
>         at java.base/java.io
> .FileOutputStream.<init>(FileOutputStream.java:155)
>         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.38da5a9d-c2ac-4a7d-8eb3-8c05b42f5c04.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:216)
>         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
> 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)
> ERROR org.irisa.genouest.logol.SequenceAnalyser  - Program exited with
> wrong status code: 127
> autopkgtest [02:15:33]: test run-unit-test
>
>
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