Bug#1026056: swi-prolog breaks logol autopkgtest: Program exited with wrong status code

[Paul Gevers]

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...@lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),



                       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





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.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  - option g called with 1799.logol
INFO org.irisa.genouest.logol.Logol  - option s called with 1799.fasta

INFO org.irisa.genouest.logol.Logol  - option dna called

Executing prolog for pre-analyse

        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..

        at org.irisa.genouest.logol.Logol.execute(Unknown Source)
        at org.irisa.genouest.logol.Logol.main(Unknown Source)

autopkgtest [02:15:33]: test run-unit-test

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: 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? 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) INFO org.irisa.genouest.logol.Logol - Using configuration file: /usr/share/logol/prolog/logol.properties INFO org.irisa.genouest.logol.Logol - No maximum solutions defined, using defaults INFO org.irisa.genouest.logol.Logol - Start analyse to create grammar analyser java.io.FileNotFoundException: /tmp/1799.logol.38da5a9d-c2ac-4a7d-8eb3-8c05b42f5c04.pre.res (No such file or directory) 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 ERROR org.irisa.genouest.logol.SequenceAnalyser - Program exited with wrong status code: 127

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