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 <elb...@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...@lists.debian.org >> User: debian...@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/
