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

[Étienne Mollier]

Hi Paul,

Paul Gevers, on 2022-10-23:
> @logol maintainers, those ERRORs look scary if the test passes with it. Is
> that just noise, or are real problems ignored?

It looks like by default, logol expects any user to be able to
drop processing results into /var/lib/logol/results, and output
processing log in /var/log/logol.  If I make them sticky world
writable, the errors go away:

	drwxrwxrwt 2 root root 40 Oct 23 08:23 /var/lib/logol/results
	drwxrwxrwt 2 root root 40 Oct 23 08:23 /var/log/logol

	calling logol with parameters -g 1799.logol -s 1799.fasta -dna
	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.731c3e5a-f513-4c97-af0e-1557d6881784.1-4.xml: 3
	INFO org.irisa.genouest.logol.Logol  - Number of output match: 3
	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.731c3e5a-f513-4c97-af0e-1557d6881784.0-4-all.xml
	calling logol with parameters -g 1799.logol -s 1799.fasta -dna
	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.1bd39463-6486-418a-be2e-7b5c0b49cee0
	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.1bd39463-6486-418a-be2e-7b5c0b49cee0
	INFO org.irisa.genouest.logol.dispatcher.LocalJobManager  - Analyse for /var/lib/logol/results//1799.fasta.1bd39463-6486-418a-be2e-7b5c0b49cee0 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.1bd39463-6486-418a-be2e-7b5c0b49cee0-XX-YY-all.xml
	INFO org.irisa.genouest.logol.utils.LogolUtils  - **** Results ****
	INFO org.irisa.genouest.logol.utils.LogolUtils  - *	/var/lib/logol/results//1799.fasta.1bd39463-6486-418a-be2e-7b5c0b49cee0.1.xml	3
	INFO org.irisa.genouest.logol.utils.LogolUtils  - ****	Total matches:	3
	INFO org.irisa.genouest.logol.dispatcher.Dispatch  - Result file is available at: /var/lib/logol/results//1799.fasta.77dfc996-bb6b-4a83-b9a9-153d73d03e97.zip

It doesn't feel ideal, but looking through the package, these
seem intended to be adjusted to specific cluster setups.  Not
sure that the default is the best, but I haven't located where
these were set in the source code in the first place.

In hope this clarifies things,
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/7, please excuse my verbosity.
On air: Cyril - Scarlet Walking
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