[Debian-med-packaging] Bug#1006384: swi-prolog breaks logol autopkgtest: Program exited with wrong status code

[olivier sallou]

ok,
after a quick look, issue is Logol is compiled against swi-prolog, and
there is an ABI issue I think, getting error:

incompatible version (file: 67, Prolog: 68)]

Recompiling logol in sid against swi-prolog 8.4.2+dfsg-2 results in correct
execution/tests.

So, 2 things:

* As swi-prolog is only a debian update (-1 to -2), I wonder why we have
this break now....
* Possible fix is to rebuild logol package against this version in sid,
with a dep requirement on swi-prolog>=8.4.2+dfsg-2. But I don't know how
this should be managed (logol in testing will still prevent swi-prolog to
go, and logol in sid won't either go to testing because will need
swi-prolog version from sid...)


Olivier


Le jeu. 24 févr. 2022 à 19:36, Paul Gevers <elbrus at debian.org> a écrit :

> 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-ci at lists.debian.org
> 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    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
>
>

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