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

Tue Mar 1 09:01:43 GMT 2022

Le lun. 28 févr. 2022 à 06:37, <dogsleg at riseup.net> a écrit :

> Dear Olivier,
>
> sorry for the delay with my message and thanks for your input.
>
> olivier sallou писал 2022-02-25 12:12:
> > 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...)
>
> It is not just Debian update. I've uploaded new upstream version of
> SWI-Prolog on Feb 15 (upgrade from 8.2.4 to 8.4.2). It is a new major
> update of stable branch of SWI-Prolog, and it breaks compatibility. As
> I can see logol tests failed already with 8.4.2+dfsg-1. There was an
> issue with ODBC support for SWI-Prolog on 32-bit platforms, so I
> uploaded
> 8.4.2+dfsg-2 fixing this issue.
>
> I think swi-prolog and (updated) logol may migrate simultaneously as it
> is the case for swi-prolog and eye (another package depending on
> swi-prolog). Otherwise, we could ask someone from Debian Release team to
> trigger the migration for the involved packages.
>
ok,
I uploaded logol 1.7.9+dfsg-2 built against swi-prolog 8.4.2 and closing
the issue with upload.
Let's see what happens for migration.

Olivier


>
> Cheers!
> Lev
>
> > 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 [1].FileOutputStream.open0(Native
> >> Method)
> >> at java.base/java.io
> >> [1].FileOutputStream.open(FileOutputStream.java:298)
> >> at java.base/java.io
> >> [1].FileOutputStream.<init>(FileOutputStream.java:237)
> >> at java.base/java.io
> >> [1].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 [1].FileInputStream.open0(Native
> >> Method)
> >> at java.base/java.io
> >> [1].FileInputStream.open(FileInputStream.java:219)
> >> at java.base/java.io
> >> [1].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
> >
> > --
> >
> > gpg key id: 4096R/326D8438  (keyring.debian.org [2])
> >
> > Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
> >
> >
> > Links:
> > ------
> > [1] http://java.io
> > [2] http://keyring.debian.org/
>


-- 

gpg key id: 4096R/326D8438  (keyring.debian.org)

Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
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