Your message dated Sat, 06 Aug 2022 16:05:11 +0000
with message-id <e1okmiz-00g9uh...@fasolo.debian.org>
and subject line Bug#1014104: fixed in mothur 1.48.0-2
has caused the Debian Bug report #1014104,
regarding mothur: autopkgtest regression: did not complete cluster.
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1014104: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1014104
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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 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
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: mothur
Source-Version: 1.48.0-2
Done: Mohammed Bilal <mdbi...@disroot.org>
We believe that the bug you reported is fixed in the latest version of
mothur, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1014...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Mohammed Bilal <mdbi...@disroot.org> (supplier of updated mothur package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sat, 06 Aug 2022 14:24:47 +0000
Source: mothur
Architecture: source
Version: 1.48.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Mohammed Bilal <mdbi...@disroot.org>
Closes: 1014104
Changes:
mothur (1.48.0-2) unstable; urgency=medium
.
* Team upload.
* Fix batch file for autopkgtest (Closes: #1014104)
* Add patch to add hardening flags
* Refresh patch
Checksums-Sha1:
c4bc1bdbc1cdf4df61d8d084a094ec78598bf5ec 2075 mothur_1.48.0-2.dsc
6987857a84248ac9520951f332420637659adc50 21540 mothur_1.48.0-2.debian.tar.xz
8796035442366d686200bbac308899502c92f37a 6867 mothur_1.48.0-2_amd64.buildinfo
Checksums-Sha256:
454363a9dce96af1af01def73f65fe9ce15ffbf53693930946a731111be977a7 2075
mothur_1.48.0-2.dsc
0c9fbbe96867636096382cacbf45c6b5d79ae8c09c08458be9dae2fe485d9944 21540
mothur_1.48.0-2.debian.tar.xz
9eda6ae215283b6cd68a91212dbc2a6cdf2ebe1f177f428ac9ef3bdcd5da3666 6867
mothur_1.48.0-2_amd64.buildinfo
Files:
0a2f7da23b03e41be64a275a967ae198 2075 science optional mothur_1.48.0-2.dsc
590b8d6207a1c176f47a8bd21eea1d70 21540 science optional
mothur_1.48.0-2.debian.tar.xz
379d782babe692b36c49ea4bbef44e0c 6867 science optional
mothur_1.48.0-2_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=Tiee
-----END PGP SIGNATURE-----
--- End Message ---
