[Debian-med-packaging] 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-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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