[Debian-med-packaging] Bug#1022253: swi-prolog breaks logol autopkgtest on s390x

Sun Oct 23 09:10:26 BST 2022

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 
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.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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