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

[Andreas Tille]

Hi Tomasz,

could you please have a look?

Kind regards

    Andreas.

Am Thu, Jun 30, 2022 at 11:42:46AM +0200 schrieb 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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