Source: mothur Version: 1.48.0-1 Severity: serious User: debian...@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 availableFor 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 16617It took 0 secs to find distances for 259 sequences. 32582 distances below cutoff 0.01.
Output File Names: HA.unique.distmothur > 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.listNo 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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