Build fails due to `robot` UNKNOWN ARG ERROR

[caufieldjh]

Describe the bug

On the most recent build attempt (sudo make all_release), this error appears during running the update query for subq patterns:

#echo "Running update query for subq patterns..."
robot --catalog catalog-v001.xml query --input tmp/phenio-full.owl --format 'owl' --update tmp/subq_update.sparql --temporary-file 'true' annotate --ontology-iri http://purl.obolibrary.org/obo/phenio/phenio-full.owl annotate -V http://purl.obolibrary.org/obo/phenio/releases/2024-02-29/phenio-full.owl --annotation owl:versionInfo 2024-02-29 --output phenio-full.owl
UNKNOWN ARG ERROR unknown command or option: --temporary-file
For details see: http://robot.obolibrary.org/errors#unknown-arg-error

To Reproduce

Run robot update with --temporary-file 'true' annotate argument.

Expected behavior

This error should not appear - or at least it hasn't previously.

ODK is the most recent version (latest, or v1.4.3)

[caufieldjh]

I think the build was just running with the wrong ODK image due to running sudo make all_release instead of sudo sh run.sh make all_release. Will close if that was the issue.

[caufieldjh]

This has started to get a bit strange - perhaps a different bug, but I'm continuing this issue because the problem happens at a similar point in the build:

robot --catalog catalog-v001.xml relax --input tmp/phenio-full-unreasoned.owl \
             annotate --ontology-iri http://purl.obolibrary.org/obo/phenio/tmp/phenio-full.owl annotate -V http://purl.obolibrary.org/obo/phenio/releases/2024-03-01/tmp/phenio-full.owl --annotation owl:versionInfo 2024-03-01 --output tmp/phenio-full.owl.tmp.owl && mv tmp/phenio-full.owl.tmp.owl tmp/phenio-full.owl
#echo "Finding subq patterns based on ../sparql/subq_construct.sparql..."
robot --catalog catalog-v001.xml query --input tmp/phenio-full.owl --tdb true --format 'owl' --query ../sparql/subq_construct.sparql tmp/phenio-full_subqs_queryresult.tmp.owl
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGBUS (0x7) at pc=0x00007f065c83d596, pid=973, tid=977
#
# JRE version: OpenJDK Runtime Environment (11.0.20.1+1) (build 11.0.20.1+1-post-Ubuntu-0ubuntu122.04)
# Java VM: OpenJDK 64-Bit Server VM (11.0.20.1+1-post-Ubuntu-0ubuntu122.04, mixed mode, sharing, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# v  ~StubRoutines::jlong_disjoint_arraycopy
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport -p%p -s%s -c%c -d%d -P%P -u%u -g%g -- %E" (or dumping to /work/src/ontology/core.973)
#
# An error report file with more information is saved as:
# /work/src/ontology/hs_err_pid973.log
Compiled method (c2)  167313 4373       4       org.apache.jena.tdb.transaction.JournalControl::replay (181 bytes)
 total in heap  [0x00007f06647ed410,0x00007f06647f03f0] = 12256
 relocation     [0x00007f06647ed588,0x00007f06647ed670] = 232
 main code      [0x00007f06647ed680,0x00007f06647eef00] = 6272
 stub code      [0x00007f06647eef00,0x00007f06647eef28] = 40
 oops           [0x00007f06647eef28,0x00007f06647eef68] = 64
 metadata       [0x00007f06647eef68,0x00007f06647ef150] = 488
 scopes data    [0x00007f06647ef150,0x00007f06647efd98] = 3144
 scopes pcs     [0x00007f06647efd98,0x00007f06647f02a8] = 1296
 dependencies   [0x00007f06647f02a8,0x00007f06647f02d0] = 40
 handler table  [0x00007f06647f02d0,0x00007f06647f02e8] = 24
 nul chk table  [0x00007f06647f02e8,0x00007f06647f03f0] = 264
Could not load hsdis-amd64.so; library not loadable; PrintAssembly is disabled
#
# If you would like to submit a bug report, please visit:
#   https://bugs.launchpad.net/ubuntu/+source/openjdk-lts
#
make: *** [phenio.Makefile:40: tmp/phenio-full_subqs_queryresult.tmp.owl] Aborted (core dumped)
make: *** Deleting file 'tmp/phenio-full_subqs_queryresult.tmp.owl'
Command exited with non-zero status 2
### DEBUG STATS ###
Elapsed time: 15:01.66
Peak memory: 14256528 kb
Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/.

That's after deleting the tmp dir.

Otherwise the error that appears is Transaction has already committed or aborted.

The error above writes out an error log but it's empty.

[caufieldjh]

I suspect the JRE error was due to interacting with a corrupt temp file - clearing out the tmp dir AND the .tdb AND all previously created artifacts appears to solve the issue.