[Debian-med-packaging] Bug#959503: salmon breaks trinityrnaseq autopkgtest: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v -shuffle died with ret 256

[Paul Gevers]

Source: salmon, trinityrnaseq
Control: found -1 salmon/1.2.1+ds1-1
Control: found -1 trinityrnaseq/2.6.6+dfsg-6
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),

With a recent upload of salmon the autopkgtest of trinityrnaseq fails in
testing when that autopkgtest is run with the binary packages of salmon
from unstable. It passes when run with only packages from testing. In
tabular form:

                       pass            fail
salmon                 from testing    1.2.1+ds1-1
trinityrnaseq          from testing    2.6.6+dfsg-6
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 salmon 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=salmon

https://ci.debian.net/data/autopkgtest/testing/amd64/t/trinityrnaseq/5248098/log.gz


We are sorry, commands in file: [FailedCommands] failed.  :-(

Error, cmd: /usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v
-shuffle  died with ret 256 at ../../Trinity line 2589.
	main::process_cmd("/usr/bin/ParaFly -c recursive_trinity.cmds -CPU 2 -v
-shuffle ") called at ../../Trinity line 3226
	main::run_partitioned_cmds("recursive_trinity.cmds") called at
../../Trinity line 2247
	main::run_recursive_trinity("/tmp/autopkgtest-lxc.v050vbja/downtmp/autopkgtest_tmp/trinity"...) called at ../../Trinity line 2009
	main::run_chrysalis("/tmp/autopkgtest-lxc.v050vbja/downtmp/autopkgtest_tmp/trinity"..., "/tmp/autopkgtest-lxc.v050vbja/downtmp/autopkgtest_tmp/trinity"..., 200, 500, "RF", "/tmp/autopkgtest-lxc.v050vbja/downtmp/autopkgtest_tmp/trinity"..., "/tmp/autopkgtest-lxc.v050vbja/downtmp/autopkgtest_tmp/trinity"...) called at ../../Trinity line 1672
	main::run_Trinity() called at ../../Trinity line 1325
	eval {...} called at ../../Trinity line 1324

Trinity run failed. Must investigate error above.
make[1]: *** [Makefile:7: test_all] Error 2
make[1]: Leaving directory
'/tmp/autopkgtest-lxc.v050vbja/downtmp/autopkgtest_tmp/trinityrnaseq/sample_data/test_Trinity_Assembly'
make: *** [Makefile:6: test_trin_assembly] Error 2

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 488 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200503/f3f9499b/attachment-0001.sig>