Your message dated Fri, 24 Jul 2020 08:25:01 +0200
with message-id <ebb99d15-8951-5598-a307-2388b1f35...@debian.org>
and subject line Re: mothur: autopkgtest regression: Segmentation fault
has caused the Debian Bug report #960873,
regarding mothur: autopkgtest regression: Segmentation fault
to be marked as done.
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960873: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960873
Debian Bug Tracking System
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--- Begin Message ---
Source: mothur
Version: 1.44.0-1
X-Debbugs-CC: debian...@lists.debian.org
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 1.44.0-1
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/5517339/log.gz
autopkgtest [19:10:00]: test run-unit-test: [-----------------------
TERM environment variable not set.
unique.seqs(fasta=HA.fasta)
command
Linux version
Using ReadLine
mothur v.1.44.0
Last updated: 05/16/2020
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.names
HA.unique.fasta
dist.seqs(fasta=HA.unique.fasta, countends=F, cutoff=0.01)
command
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
cluster(method=furthest, column=HA.unique.dist, name=HA.names,
cutoff=0.01, precision=1000)
command
mothur > cluster(method=furthest, column=HA.unique.dist, name=HA.names,
cutoff=0.01, precision=1000)
Using 2 processors.
unique 154 211 18 2 6 0 4 2 0
2 0 0 0 1 0 0 0 0 2
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0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1
0.001 155 161 28 5 3 4 2 4 0
0 1 0 1 0 1 0 0 0 0
2 0 0 1 0 0 0 0 0 0
0 0
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0 0 0 0 0 0 1
0.002 206 56 9 8 2 0 4 2 2
0 0 0 0 0 2 0 0 0 0
1 1 0 0 0 0 0 1 0 0
0 1 0
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1
0.003 236 26 4 2 1 1 0 2 2
1 0 0 0 0 1 1 0 0 0
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0 0 0 0 0 0 0 0 0 0
0 0 0 0 1
0.004 270 15 3 0 1 0 0 1 1
0 0 0 0 0 1 0 0 0 0
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0 0 0
0 0 0 0 0 1 1 0 0 0
0 0 0 0 0 0 0 0 1 0
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0 0 0 0 0 0 0 0 0 0
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0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 1
0.005 272 7 2 0 0 0 0 1 1
0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 0 0 0 0 0
0 0 0
0 0 0 0 0 0 0 2 0 0
0 0 0 0 0 0 0 0 0 1
0 0 0 0 0 0 0 0 0 0
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0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 1
0.006 274 5 1 0 0 0 0 0 1
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0 0 0 0 0 0 0 0 0 0
0 0 0
0 0 0 0 0 0 0 0 1 0
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0 0 0 0 1 0 0 0 0 0
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0 0 0 0 0 0 0 0 0 0
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0 0 0 0 0 0
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0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1
0.007 274 5 1 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0
0 0 0 0 0 0 0 0 1 0
0 0 0 0 0 0 0 0 0 0
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0 0 0 0 0 0 0 0 0 0
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0.008 552 3 2 0 0 0 0 0 0
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0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1
0.009 592 3 2 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0 0
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0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
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0 0 0 0 0 0 0 0 0 0
1
It took 0 seconds to cluster
Output File Names:
HA.unique.fn.sabund
HA.unique.fn.rabund
HA.unique.fn.list
summary.single(list=HA.unique.fn.list, calc=nseqs-sobs-chao,
label=unique-0.001-0.003-0.005-0.008)
command
mothur > summary.single(list=HA.unique.fn.list, calc=nseqs-sobs-chao,
label=unique-0.001-0.003-0.005-0.008)
unique
0.001
0.003
0.005
0.008
Output File Names:
HA.unique.fn.summary
heatmap.bin(scale=linear, label=unique-0.001-0.003)
command
mothur > heatmap.bin(scale=linear, label=unique-0.001-0.003)
Using HA.unique.fn.list as input file for the list parameter.
Segmentation fault
autopkgtest [19:10:00]: test run-unit-test: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Version: 1.44.2-1
Hi all,
On 17-05-2020 20:51, Paul Gevers wrote:
> 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 1.44.0-1
> all others from testing from testing
Seems fixed in the latest upload.
Paul
signature.asc
Description: OpenPGP digital signature
--- End Message ---
