<div dir="ltr">ok,<div>after a quick look, issue is Logol is compiled against swi-prolog, and there is an ABI issue I think, getting error:</div><div><br></div><div>incompatible version (file: 67, Prolog: 68)]<br></div><div><br></div><div>Recompiling logol in sid against swi-prolog 8.4.2+dfsg-2 results in correct execution/tests.</div><div><br></div><div>So, 2 things:</div><div><br></div><div>* As swi-prolog is only a debian update (-1 to -2), I wonder why we have this break now....</div><div>* 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...)</div><div><br></div><div><br></div><div>Olivier</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 24 févr. 2022 à 19:36, Paul Gevers <<a href="mailto:elbrus@debian.org" target="_blank">elbrus@debian.org</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Source: swi-prolog, logol<br>
Control: found -1 swi-prolog/8.4.2+dfsg-2<br>
Control: found -1 logol/1.7.9+dfsg-1<br>
Severity: serious<br>
Tags: sid bookworm<br>
X-Debbugs-CC: <a href="mailto:debian-ci@lists.debian.org" target="_blank">debian-ci@lists.debian.org</a><br>
User: <a href="mailto:debian-ci@lists.debian.org" target="_blank">debian-ci@lists.debian.org</a><br>
Usertags: breaks needs-update<br>
<br>
Dear maintainer(s),<br>
<br>
With a recent upload of swi-prolog the autopkgtest of logol fails in <br>
testing when that autopkgtest is run with the binary packages of <br>
swi-prolog from unstable. It passes when run with only packages from <br>
testing. In tabular form:<br>
<br>
pass fail<br>
swi-prolog from testing 8.4.2+dfsg-2<br>
logol from testing 1.7.9+dfsg-1<br>
all others from testing from testing<br>
<br>
I copied some of the output at the bottom of this report.<br>
<br>
Currently this regression is blocking the migration of swi-prolog to <br>
testing [1]. Due to the nature of this issue, I filed this bug report <br>
against both packages. Can you please investigate the situation and <br>
reassign the bug to the right package?<br>
<br>
More information about this bug and the reason for filing it can be found on<br>
<a href="https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation" rel="noreferrer" target="_blank">https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation</a><br>
<br>
Paul<br>
<br>
[1] <a href="https://qa.debian.org/excuses.php?package=swi-prolog" rel="noreferrer" target="_blank">https://qa.debian.org/excuses.php?package=swi-prolog</a><br>
<br>
<a href="https://ci.debian.net/data/autopkgtest/testing/amd64/l/logol/19529867/log.gz" rel="noreferrer" target="_blank">https://ci.debian.net/data/autopkgtest/testing/amd64/l/logol/19529867/log.gz</a><br>
<br>
calling logol with parameters -g 1799.logol -s 1799.fasta -dna<br>
log4j:ERROR setFile(null,true) call failed.<br>
java.io.FileNotFoundException: /var/log/logol/logol.log (Permission denied)<br>
at java.base/<a href="http://java.io" target="_blank">java.io</a>.FileOutputStream.open0(Native Method)<br>
at java.base/<a href="http://java.io" target="_blank">java.io</a>.FileOutputStream.open(FileOutputStream.java:298)<br>
at java.base/<a href="http://java.io" target="_blank">java.io</a>.FileOutputStream.<init>(FileOutputStream.java:237)<br>
at java.base/<a href="http://java.io" target="_blank">java.io</a>.FileOutputStream.<init>(FileOutputStream.java:158)<br>
at org.apache.log4j.FileAppender.setFile(FileAppender.java:294)<br>
at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)<br>
at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)<br>
at <br>
org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)<br>
at <br>
org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)<br>
at <br>
org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)<br>
at <br>
org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)<br>
at <br>
org.apache.log4j.PropertyConfigurator.parseCatsAndRenderers(PropertyConfigurator.java:672)<br>
at <br>
org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:516)<br>
at <br>
org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)<br>
at <br>
org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)<br>
at org.apache.log4j.LogManager.<clinit>(LogManager.java:127)<br>
at org.apache.log4j.Logger.getLogger(Logger.java:117)<br>
at org.irisa.genouest.logol.Logol.<clinit>(Unknown Source)<br>
For help, use option -h<br>
INFO org.irisa.genouest.logol.Logol - Using configuration file: <br>
/usr/share/logol/prolog/logol.properties<br>
INFO org.irisa.genouest.logol.Logol - option g called with 1799.logol<br>
INFO org.irisa.genouest.logol.Logol - option s called with 1799.fasta<br>
INFO org.irisa.genouest.logol.Logol - No maximum solutions defined, <br>
using defaults<br>
INFO org.irisa.genouest.logol.Logol - option dna called<br>
INFO org.irisa.genouest.logol.Logol - Start analyse to create grammar <br>
analyser<br>
Executing prolog for pre-analyse<br>
java.io.FileNotFoundException: <br>
/tmp/1799.logol.be129f0a-eeb3-4c10-a744-e5ccabb1087e.pre.res (No such <br>
file or directory)<br>
at java.base/<a href="http://java.io" target="_blank">java.io</a>.FileInputStream.open0(Native Method)<br>
at java.base/<a href="http://java.io" target="_blank">java.io</a>.FileInputStream.open(FileInputStream.java:219)<br>
at java.base/<a href="http://java.io" target="_blank">java.io</a>.FileInputStream.<init>(FileInputStream.java:157)<br>
at java.base/java.io.FileReader.<init>(FileReader.java:75)<br>
at org.irisa.genouest.logol.Logol.loadVariables2Postpone(Unknown Source)<br>
at org.irisa.genouest.logol.Logol.generatePreAnalysis(Unknown Source)<br>
at org.irisa.genouest.logol.Logol.analyse(Unknown Source)<br>
at org.irisa.genouest.logol.Logol.execute(Unknown Source)<br>
at org.irisa.genouest.logol.Logol.main(Unknown Source)<br>
INFO org.irisa.genouest.logol.Logol - Analyse in progress..<br>
WARN org.irisa.genouest.logol.SequenceAnalyser - Path to suffix search <br>
tool is not set in system environment. Will try to execute directly but <br>
may fail if not in PATH of current user<br>
ERROR org.irisa.genouest.logol.SequenceAnalyser - Program exited with <br>
wrong status code: 134<br>
Exception in thread "main" org.irisa.genouest.logol.GrammarException: <br>
ERROR: Coudld not execute program: Program exited with wrong status code<br>
at org.irisa.genouest.logol.Logol.execute(Unknown Source)<br>
at org.irisa.genouest.logol.Logol.main(Unknown Source)<br>
autopkgtest [10:27:07]: test run-unit-test<br>
<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><pre cols="72">gpg key id: 4096R/326D8438 (<a href="http://keyring.debian.org/" target="_blank">keyring.debian.org</a>)</pre><pre cols="72">Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438</pre></div>