<div dir="ltr"><div dir="ltr"><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le lun. 28 févr. 2022 à 06:37, <<a href="mailto:dogsleg@riseup.net">dogsleg@riseup.net</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">Dear Olivier,<br>
<br>
sorry for the delay with my message and thanks for your input.<br>
<br>
olivier sallou писал 2022-02-25 12:12:<br>
> ok,<br>
> after a quick look, issue is Logol is compiled against swi-prolog, and<br>
> there is an ABI issue I think, getting error:<br>
> <br>
> incompatible version (file: 67, Prolog: 68)]<br>
> <br>
> Recompiling logol in sid against swi-prolog 8.4.2+dfsg-2 results in<br>
> correct execution/tests.<br>
> <br>
> So, 2 things:<br>
> <br>
> * As swi-prolog is only a debian update (-1 to -2), I wonder why we<br>
> have this break now....<br>
> * Possible fix is to rebuild logol package against this version in<br>
> sid, with a dep requirement on swi-prolog>=8.4.2+dfsg-2. But I don't<br>
> know how this should be managed (logol in testing will still prevent<br>
> swi-prolog to go, and logol in sid won't either go to testing because<br>
> will need swi-prolog version from sid...)<br>
<br>
It is not just Debian update. I've uploaded new upstream version of<br>
SWI-Prolog on Feb 15 (upgrade from 8.2.4 to 8.4.2). It is a new major<br>
update of stable branch of SWI-Prolog, and it breaks compatibility. As<br>
I can see logol tests failed already with 8.4.2+dfsg-1. There was an<br>
issue with ODBC support for SWI-Prolog on 32-bit platforms, so I<br>
uploaded<br>
8.4.2+dfsg-2 fixing this issue.<br>
<br>
I think swi-prolog and (updated) logol may migrate simultaneously as it<br>
is the case for swi-prolog and eye (another package depending on<br>
swi-prolog). Otherwise, we could ask someone from Debian Release team to<br>
trigger the migration for the involved packages.<br></blockquote><div>ok,</div><div>I uploaded logol 1.7.9+dfsg-2 built against swi-prolog 8.4.2 and closing the issue with upload.</div><div>Let's see what happens for migration.</div><div><br></div><div>Olivier</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
Cheers!<br>
Lev<br>
<br>
> Le jeu. 24 févr. 2022 à 19:36, Paul Gevers <<a href="mailto:elbrus@debian.org" target="_blank">elbrus@debian.org</a>> a<br>
> écrit :<br>
> <br>
>> 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>
>><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>
>><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>
>><br>
>> testing [1]. Due to the nature of this issue, I filed this bug<br>
>> 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<br>
>> found on<br>
>><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>
>><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<br>
>> denied)<br>
>> at java.base/<a href="http://java.io" rel="noreferrer" target="_blank">java.io</a> [1].FileOutputStream.open0(Native<br>
>> Method)<br>
>> at java.base/<a href="http://java.io" rel="noreferrer" target="_blank">java.io</a><br>
>> [1].FileOutputStream.open(FileOutputStream.java:298)<br>
>> at java.base/<a href="http://java.io" rel="noreferrer" target="_blank">java.io</a><br>
>> [1].FileOutputStream.<init>(FileOutputStream.java:237)<br>
>> at java.base/<a href="http://java.io" rel="noreferrer" target="_blank">java.io</a><br>
>> [1].FileOutputStream.<init>(FileOutputStream.java:158)<br>
>> at<br>
>> org.apache.log4j.FileAppender.setFile(FileAppender.java:294)<br>
>> at<br>
>> org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165)<br>
>> at<br>
>><br>
> org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307)<br>
>> at<br>
>><br>
> org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172)<br>
>> at<br>
>><br>
> org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104)<br>
>> at<br>
>><br>
> org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:842)<br>
>> at<br>
>><br>
> org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)<br>
>> at<br>
>><br>
> org.apache.log4j.PropertyConfigurator.parseCatsAndRenderers(PropertyConfigurator.java:672)<br>
>> at<br>
>><br>
> org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:516)<br>
>> at<br>
>><br>
> org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)<br>
>> at<br>
>><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<br>
>> 1799.logol<br>
>> INFO org.irisa.genouest.logol.Logol - option s called with<br>
>> 1799.fasta<br>
>> INFO org.irisa.genouest.logol.Logol - No maximum solutions defined,<br>
>><br>
>> using defaults<br>
>> INFO org.irisa.genouest.logol.Logol - option dna called<br>
>> INFO org.irisa.genouest.logol.Logol - Start analyse to create<br>
>> 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<br>
>> such<br>
>> file or directory)<br>
>> at java.base/<a href="http://java.io" rel="noreferrer" target="_blank">java.io</a> [1].FileInputStream.open0(Native<br>
>> Method)<br>
>> at java.base/<a href="http://java.io" rel="noreferrer" target="_blank">java.io</a><br>
>> [1].FileInputStream.open(FileInputStream.java:219)<br>
>> at java.base/<a href="http://java.io" rel="noreferrer" target="_blank">java.io</a><br>
>> [1].FileInputStream.<init>(FileInputStream.java:157)<br>
>> at java.base/java.io.FileReader.<init>(FileReader.java:75)<br>
>> at<br>
>> org.irisa.genouest.logol.Logol.loadVariables2Postpone(Unknown<br>
>> Source)<br>
>> at<br>
>> 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<br>
>> search<br>
>> tool is not set in system environment. Will try to execute directly<br>
>> but<br>
>> may fail if not in PATH of current user<br>
>> ERROR org.irisa.genouest.logol.SequenceAnalyser - Program exited<br>
>> with<br>
>> wrong status code: 134<br>
>> Exception in thread "main"<br>
>> org.irisa.genouest.logol.GrammarException:<br>
>> ERROR: Coudld not execute program: Program exited with wrong status<br>
>> 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>
> -- <br>
> <br>
> gpg key id: 4096R/326D8438 (<a href="http://keyring.debian.org" rel="noreferrer" target="_blank">keyring.debian.org</a> [2])<br>
> <br>
> Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438<br>
> <br>
> <br>
> Links:<br>
> ------<br>
> [1] <a href="http://java.io" rel="noreferrer" target="_blank">http://java.io</a><br>
> [2] <a href="http://keyring.debian.org/" rel="noreferrer" target="_blank">http://keyring.debian.org/</a><br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><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></div>