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

[dogsleg at riseup.net]

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.

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/