[Debian-med-packaging] Bug#1014104: mothur: autopkgtest regression: did not complete cluster.

[Paul Gevers]

Source: mothur
Version: 1.48.0-1
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainer(s),

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

                        pass            fail
mothur                 from testing    1.48.0-1
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 to testing [1]. Can 
you please investigate the situation and fix it?

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=mothur

https://ci.debian.net/data/autopkgtest/testing/amd64/m/mothur/23197987/log.gz

Linux version

Using ReadLine
mothur v.1.48.0
Last updated: 5/20/22
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, 
platform-independent, community-supported software for describing and 
comparing microbial communities. Appl Environ Microbiol, 2009. 
75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at 
https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Batch Mode



mothur > unique.seqs(fasta=HA.fasta)
599	259

Output File Names: HA.unique.fasta
HA.count_table


mothur > dist.seqs(fasta=HA.unique.fasta, countends=F, cutoff=0.01)

Using 2 processors.

Sequence	Time	Num_Dists_Below_Cutoff
0	0	0
200	0	3443
100	0	5025
258	0	15965
182	0	16617

It took 0 secs to find distances for 259 sequences. 32582 distances 
below cutoff 0.01.


Output File Names: HA.unique.dist


mothur > cluster(method=furthest, column=HA.unique.dist, name=HA.names, 
cutoff=0.01, precision=1000)
Unable to open HA.names. Trying mothur's executable directory HA.names.
Unable to open HA.names.
Unable to open HA.names

Using 2 processors.
[ERROR]: did not complete cluster.

mothur > summary.single(list=HA.unique.fn.list, calc=nseqs-sobs-chao, 
label=unique-0.001-0.003-0.005-0.008)
Unable to open HA.unique.fn.list. Trying mothur's executable directory 
HA.unique.fn.list.
Unable to open HA.unique.fn.list.
Unable to open HA.unique.fn.list
No valid current files. You must provide a list, sabund, rabund or 
shared file before you can use the collect.single command.
[ERROR]: did not complete summary.single.

mothur > heatmap.bin(scale=linear, label=unique-0.001-0.003)
No valid current files. You must provide a list, sabund, rabund, 
relabund or shared file.
[ERROR]: did not complete heatmap.bin.

mothur > rarefaction.single(calc=sobs-chao, label=unique-0.001-0.003, 
freq=10)
No valid current files. You must provide a list, sabund, rabund or 
shared file before you can use the collect.single command.

Using 2 processors.
[ERROR]: did not complete rarefaction.single.

mothur > quit()


It took 0 seconds to run 7 commands from test.batch batch file.

Logfile : mothur.1656579650.logfile



************************************************************
************************************************************
************************************************************
Detected 4 [ERROR] messages, please review.
************************************************************
************************************************************
************************************************************
autopkgtest [09:00:51]: test run-unit-test

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