Your message dated Wed, 6 May 2020 16:21:19 +0200
with message-id <0bf67939-4c88-24ff-07ca-a2d63a4b7...@gmail.com>
and subject line Re: salmon breaks trinityrnaseq autopkgtest: /usr/bin/ParaFly
-c recursive_trinity.cmds -CPU 2 -v -shuffle died with ret 256
has caused the Debian Bug report #959503,
regarding salmon breaks trinityrnaseq autopkgtest: /usr/bin/ParaFly -c
recursive_trinity.cmds -CPU 2 -v -shuffle died with ret 256
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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959503: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959503
Debian Bug Tracking System
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--- Begin Message ---
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...@lists.debian.org
User: debian...@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
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Version: trinityrnaseq/2.10.0+dfsg-1
Fixed by a newer TrinityRNASeq release, thanks!
signature.asc
Description: OpenPGP digital signature
--- End Message ---
