Your message dated Mon, 07 Feb 2022 12:05:31 +0000
with message-id <[email protected]>
and subject line Bug#1004506: fixed in theseus 3.3.0-11
has caused the Debian Bug report #1004506,
regarding muscle breaks theseus autopkgtest: Unknown option maxiters
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.
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--
1004506: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1004506
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: muscle, theseus
Control: found -1 muscle/1:5.1-1
Control: found -1 theseus/3.3.0-10
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: [email protected]
User: [email protected]
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of muscle the autopkgtest of theseus fails in
testing when that autopkgtest is run with the binary packages of muscle
from unstable. It passes when run with only packages from testing. In
tabular form:
pass fail
muscle from testing 1:5.1-1
theseus from testing 3.3.0-10
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 of muscle to testing
[1]. Due to the nature of this issue, I filed this bug report against
both packages. Can you please investigate the situation and reassign the
bug to the right package?
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=muscle
https://ci.debian.net/data/autopkgtest/testing/amd64/t/theseus/18786643/log.gz
[1;31m< BEGIN THESEUS 3.3.0 >[0m
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=I
I [1;36mTHESEUS[0m: Maximum likelihood multiple
superpositioning I
I=-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===I
Detected 48 CPUs ... Reading pdb file ... Successfully read
10 models and/or structures Selecting coordinates for superposition
... Calculating superposition transformations ... Calculating
statistics ... Calculating likelihood statistics ... 10 models
superimposed in 2.1 ms * Classical LS pairwise <RMSD>
1.87300
* Least-squares <sigma> 0.72541
* Maximum Likelihood <sigma> 0.39551
~ Marginal Log Likelihood -4487.32
~ AIC -5223.64
~ BIC -7333.12
+ Omnibus chi^2 0.95 (P:9.98e-01)
+ Hierarchical var (2.34e-01, 1.50e+00) chi^2 0.76 (P:7.91e-01)
+ Rotational, translational, covar chi^2 0.95 (P:9.98e-01)
+ Hierarchical minimum var (sigma) 1.34e-02 (1.16e-01)
< skewness 0.03 (P:3.00e-01)
< skewness Z-value 1.04
< kurtosis 0.16 (P:1.28e-02)
< kurtosis Z-value 2.49
* Data pts = 5940, Free params = 655, D/P = 9.1 * Median
structure = #8
* N(total) = 1980, N(atoms) = 198, N(structures) = 10
Total rounds = 15
Converged to a fractional precision of 5.2e-08
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I
Transforming coordinates ... Writing transformations file ...
Writing transformed coordinates PDB file ... Writing average
coordinate file ... Done.
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I
[1;31m< END THESEUS 3.3.0 >[0m
[1;31m< BEGIN THESEUS 3.3.0 >[0m
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=I
I [1;36mTHESEUS[0m: Maximum likelihood multiple
superpositioning I
I=-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===I
Detected 48 CPUs ... Reading 10 pdb files ... Successfully
read 10 models and/or structures Reading multiple sequence alignment
... Calculating superposition transformations ... Calculating
statistics ... Calculating likelihood statistics ... 10 models
superimposed in 2.2 ms * Classical LS pairwise <RMSD>
0.80299
* Least-squares <sigma> 0.32968
* Maximum Likelihood <sigma> 0.21859
~ Marginal Log Likelihood -271.63
~ AIC -712.02
~ BIC -1841.58
+ Omnibus chi^2 7.68 (P:0.00e+00)
+ Hierarchical var (7.16e-02, 1.50e+00) chi^2 1.42 (P:8.53e-02)
+ Rotational, translational, covar chi^2 7.73 (P:0.00e+00)
+ Hierarchical minimum var (sigma) 4.09e-03 (6.40e-02)
< skewness -0.10 (P:1.45e-02)
< skewness Z-value 2.44
< kurtosis 2.83 (P:2.15e-240)
< kurtosis Z-value 33.11
* Data pts = 3270, Free params = 388, D/P = 8.4 * Median
structure = #8
* N(total) = 1090, N(atoms) = 109, N(structures) = 10
Total rounds = 17
Converged to a fractional precision of 7.1e-08
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I
Transforming coordinates ... Writing transformations file ...
Writing transformed coordinates PDB file ... Writing average
coordinate file ... Done.
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I
[1;31m< END THESEUS 3.3.0 >[0m
[1;31m< BEGIN THESEUS 3.3.0 >[0m
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=I
I [1;36mTHESEUS[0m: Maximum likelihood multiple
superpositioning I
I=-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===I
Detected 48 CPUs ... Reading 10 pdb files ... Successfully
read 10 models and/or structures Reading multiple sequence alignment
... Calculating superposition transformations ... Calculating
statistics ... Calculating likelihood statistics ... 10 models
superimposed in 2.4 ms * Classical LS pairwise <RMSD>
0.80299
* Least-squares <sigma> 0.32968
* Maximum Likelihood <sigma> 0.21859
~ Marginal Log Likelihood -271.63
~ AIC -712.02
~ BIC -1841.58
+ Omnibus chi^2 7.68 (P:0.00e+00)
+ Hierarchical var (7.16e-02, 1.50e+00) chi^2 1.42 (P:8.53e-02)
+ Rotational, translational, covar chi^2 7.73 (P:0.00e+00)
+ Hierarchical minimum var (sigma) 4.09e-03 (6.40e-02)
< skewness -0.10 (P:1.45e-02)
< skewness Z-value 2.44
< kurtosis 2.83 (P:2.15e-240)
< kurtosis Z-value 33.11
* Data pts = 3270, Free params = 388, D/P = 8.4 * Median
structure = #8
* N(total) = 1090, N(atoms) = 109, N(structures) = 10
Total rounds = 17
Converged to a fractional precision of 7.1e-08
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I
Transforming coordinates ... Writing transformations file ...
Writing transformed coordinates PDB file ... Writing average
coordinate file ... Done.
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I
[1;31m< END THESEUS 3.3.0 >[0m
PDBs for superpositioning: d1cih__.pdb d1crj__.pdb d1csu__.pdb
d1csx__.pdb d1kyow_.pdb d1lfma_.pdb d1m60a_.pdb d1u74d_.pdb d1yeb__.pdb
d2pcbb_.pdb
[1;31m< BEGIN THESEUS 3.3.0 >[0m
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=I
I [1;36mTHESEUS[0m: Maximum likelihood multiple
superpositioning I
I=-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===I
Detected 48 CPUs ... Reading 10 pdb files ... Writing FASTA
format .fst files (10) ... 1 d1cih__.pdb.fst (108 aa)
2 d1crj__.pdb.fst (108 aa)
3 d1csu__.pdb.fst (108 aa)
4 d1csx__.pdb.fst (108 aa)
5 d1kyow_.pdb.fst (108 aa)
6 d1lfma_.pdb.fst (103 aa)
7 d1m60a_.pdb.fst (104 aa)
8 d1u74d_.pdb.fst (108 aa)
9 d1yeb__.pdb.fst (108 aa)
10 d2pcbb_.pdb.fst (104 aa)
Done.
I===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-==I
[1;31m< END THESEUS 3.3.0 >[0m
/usr/bin/muscle -maxiters 32 -in theseus.fasta -out theseus.aln -clwstrict
Invalid command line
Unknown option maxiters
ERROR: Sequence alignment failed: no alignment file.
Usage: /usr/bin/theseus_align [theseus_options] -f pdbfile1.pdb
pdbfile2.pdb ...
autopkgtest [22:50:37]: test run-unit-test
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: theseus
Source-Version: 3.3.0-11
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
theseus, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated theseus 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 30 Jan 2022 17:18:29 +0100
Source: theseus
Architecture: source
Version: 3.3.0-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1004506
Changes:
theseus (3.3.0-11) unstable; urgency=medium
.
* Adapt theseus_align to muscle version 5
Closes: #1004506
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