Bug#1022253: swi-prolog breaks logol autopkgtest on s390x

Paul Gevers Sun, 23 Oct 2022 01:15:16 -0700

Hi Lev,

On 23-10-2022 09:40, Lev Lamberov wrote:

I'm not sure it is the solution, it needs testing. The change in
swi-prolog concerns pre-compiled prolog source code, when there is no
pre-complied prolog code rebuilt is not needed. SWI-Prolog supports
three different kinds of pre-compilation, at least one of them was
affected and another was not. The mentioned endiannes bug can be found
in BTS, #1006818 [bts].

I just ran the autopkgtest with a rebuild logol on s390x, see below. Does that help?

@logol maintainers, those ERRORs look scary if the test passes with it. Is that just noise, or are real problems ignored?


Paul

autopkgtest [04:01:35]: test run-unit-test: [-----------------------
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:298) at java.base/java.io.FileOutputStream.<init>(FileOutputStream.java:237) at java.base/java.io.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
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 INFO org.irisa.genouest.logol.Logol - /tmp//1799.logol.a9b0dfe5-5a3c-49d8-9364-8a42339e61ac.1-4.xml: 3

INFO org.irisa.genouest.logol.Logol  - Number of output match: 3

ERROR org.irisa.genouest.logol.utils.LogolUtils - /var/lib/logol/results/1799.logol.a9b0dfe5-5a3c-49d8-9364-8a42339e61ac.0-4-all.xml (Permission denied)

INFO org.irisa.genouest.logol.Logol  - JOB OVER !!!
INFO org.irisa.genouest.logol.Logol  - RESULT FILES ARE AVAILABLE:

INFO org.irisa.genouest.logol.Logol - - /var/lib/logol/results//1799.logol.a9b0dfe5-5a3c-49d8-9364-8a42339e61ac.0-4-all.xml

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 org.apache.log4j.FileAppender.setFile(FileAppender.java:294)

        at org.apache.log4j.LogManager.<clinit>(LogManager.java:127)
        at org.apache.log4j.Logger.getLogger(Logger.java:117)

at org.irisa.genouest.logol.dispatcher.Dispatch.<clinit>(Unknown Source)

For help, use option -h
mod1()==>REP1:{_MASEQ0,#[2,2]},REP2:{?MASEQ0}:{$$[2,2]}

INFO org.irisa.genouest.logol.dispatcher.Dispatch - Sequence 1 splitted in 1 parts INFO org.irisa.genouest.logol.dispatcher.Dispatch - Add sequence for treatment: /var/lib/logol/results//1799.fasta.fe26fb1c-9d69-4aa9-a52f-807cd09ab31a

INFO org.irisa.genouest.logol.dispatcher.Dispatch  - Args:  -sequenceID 1
INFO org.irisa.genouest.logol.dispatcher.LocalJobManager  - Run jobs locally

INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Analyse sequence /var/lib/logol/results//1799.fasta.fe26fb1c-9d69-4aa9-a52f-807cd09ab31a ERROR org.irisa.genouest.logol.dispatcher.StreamGobbler - ERROR org.irisa.genouest.logol.utils.LogolUtils - /var/lib/logol/results/1799.fasta.fe26fb1c-9d69-4aa9-a52f-807cd09ab31a.1.xml (Permission denied) INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Analyse for /var/lib/logol/results//1799.fasta.fe26fb1c-9d69-4aa9-a52f-807cd09ab31a is over INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Each sequence in bank resulted in a specific result file. INFO org.irisa.genouest.logol.dispatcher.LocalJobManager - Result file is available in work directory : /var/lib/logol/results//1799.fasta.fe26fb1c-9d69-4aa9-a52f-807cd09ab31a-XX-YY-all.xml

INFO org.irisa.genouest.logol.utils.LogolUtils  - **** Results ****

ERROR org.irisa.genouest.logol.utils.LogolUtils - /var/lib/logol/results/1799.fasta.fe26fb1c-9d69-4aa9-a52f-807cd09ab31a.1.xml (No such file or directory) INFO org.irisa.genouest.logol.utils.LogolUtils - * /var/lib/logol/results//1799.fasta.fe26fb1c-9d69-4aa9-a52f-807cd09ab31a.1.xml 0

INFO org.irisa.genouest.logol.utils.LogolUtils  - ****  Total matches:  0

ERROR org.irisa.genouest.logol.utils.LogolUtils - Error during zip file creation: /var/lib/logol/results/1799.fasta.681bbd09-ea70-4707-88bb-5e54adcab7e2.zip (Permission denied) INFO org.irisa.genouest.logol.dispatcher.Dispatch - Result file is available at: /var/lib/logol/results//1799.fasta.681bbd09-ea70-4707-88bb-5e54adcab7e2.zip

autopkgtest [04:01:37]: test run-unit-test: -----------------------]

autopkgtest [04:01:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -

run-unit-test        PASS

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Bug#1022253: swi-prolog breaks logol autopkgtest on s390x

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