Your message dated Fri, 18 Dec 2020 09:52:00 +0000
with message-id <e1kqcqa-00082n...@fasolo.debian.org>
and subject line Bug#977621: fixed in murasaki 1.68.6-11
has caused the Debian Bug report #977621,
regarding murasaki: autopkgtest armhf regression: 6660 Bus error mbfa $f
--fasta > testfile
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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977621: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=977621
Debian Bug Tracking System
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--- Begin Message ---
Source: murasaki
Version: 1.68.6-10
X-Debbugs-CC: debian...@lists.debian.org
Severity: serious
User: debian...@lists.debian.org
Usertags: regression
Dear maintainer(s),
With a recent upload of murasaki the autopkgtest of murasaki fails in
testing when that autopkgtest is run with the binary packages of
murasaki from unstable. It passes when run with only packages from
testing and on all other architectures that we test for. In tabular form:
pass fail
murasaki from testing 1.68.6-10 on armhf
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=murasaki
https://ci.debian.net/data/autopkgtest/testing/armhf/m/murasaki/8582325/log.gz
autopkgtest [19:57:51]: test run-unit-test: [-----------------------
Test Murasaki on NZ_GG705055.fna
Created output directory:
/tmp/autopkgtest-lxc.razmgtoz/downtmp/autopkgtest_tmp/output
Verbosity level is: 0
Writing to: output/test
Pattern is: 101
Max usable hash bits: 27
Hit filter is: 0
Hash table type is: EcoHash
Hashing every: 1 base
Histogram detail is: 0
Hashing function is: 3
Collision profiling is: disabled
Repeats are: unmasked
Mergefilter is at: 100
Random seed: 1606939072 (automatic)
Bitscore output: on
Leave status records: no
Join neighbors is: off
Target memory is: 3.12 GB
Retain members is: true
Store repeatmap? yes
Reverse complement data is generated on the fly
Rifts allowed: 0
Fuzzy Extension: yes
Score by minimum pair: yes
Gapped anchors: no
Large sequence support is: enabled => seqpos is 4 bytes
Murasaki version 1.68.6 (LARGESEQ)
Loading NZ_GG705055.fna
Read 398859bp (389.51 KBp) in 0.035 seconds (11.0 MBp/s)
Done with forward strand (410644bp). Preparing reverse complement...
<-> Reversing metdata.
Done.
Seq NZ_GG705055.fna loaded. 401.02 KB
Loading NZ_GG705055.gbk
Read 398859bp (389.51 KBp) in 0.048 seconds (7.9 MBp/s)
Done with forward strand (410644bp). Preparing reverse complement...
<-> Reversing metdata.
Done.
Seq NZ_GG705055.gbk loaded. 401.02 KB
Sequence loading took: 0.083 seconds
Forward frequencies: A:28.0367% C:23.1004% G:20.9036% T:27.9593%
Global base frequencies: A/T:55.996% C/G:44.004%
Pat: 3 bases long with weight 2
1 101
Computing hash parameters...
Using 4 hashbits
0%......... (T -0.170 seconds) ETA: Wed Dec 2 19:57:52 2020
10%......... (T -0.152 seconds) ETA: Wed Dec 2 19:57:52 2020
20%......... (T -0.133 seconds) ETA: Wed Dec 2 19:57:52 2020
30%......... (T -0.114 seconds) ETA: Wed Dec 2 19:57:52 2020
40%......... (T -0.095 seconds) ETA: Wed Dec 2 19:57:52 2020
50%......... (T -0.076 seconds) ETA: Wed Dec 2 19:57:52 2020
60%......... (T -0.057 seconds) ETA: Wed Dec 2 19:57:52 2020
70%......... (T -0.038 seconds) ETA: Wed Dec 2 19:57:52 2020
80%......... (T -0.017 seconds) ETA: Wed Dec 2 19:57:52 2020
91%........
Acceptable hash function found after 1000 cycles.
Best uses 2/2 bases and has 0 empties from 2 inputs.
Score: 0.925992 (cf. worst: -4.54276)
Entropy: high: 1 lo: 1 total: 2 bases (mean: 1 stddev: 0)
Total correlation penalty: 0
Post cleanup: w[0]>>13 ^ w[0]>>14 {2}
10
==
w[ 0]>>13: -.C
w[ 0]>>14: A.-
Ecolist (optimistic): (seqbits: 2 idxbits: 20 minBlocks: 1 initblocks: 1)
Ecolist (optimistic): Expcted entries per list: 17
Ecolist (optimistic): Minimum chunks per list: 1
Would take minimum 128.000000 bytes to make perfect hash.
Hashing 1.52 MB of sequence requires:
~ linear (in seq length) hashing cost of 4.18 MB
~ linear (in seq length) expected anchor cost of 18.80 MB
Initial hash table uses: 128 bytes (4 bits, 16 entries)
Expected memory usage (without anchors): 4.18 MB
Expected memory usage (with anchors): 22.98 MB
Hash parameters computed in 0.187 seconds
Creating storage structures: 16 entries in 128 bytes space.
Storage structures created in: 0.000 seconds
Hashing NZ_GG705055.fna forwards
0%......... (T -0.050 seconds) ETA: Wed Dec 2 19:57:52 2020
10%......... (T -0.047 seconds) ETA: Wed Dec 2 19:57:52 2020
20%......... (T -0.043 seconds) ETA: Wed Dec 2 19:57:52 2020
30%......... (T -0.037 seconds) ETA: Wed Dec 2 19:57:52 2020
40%......... (T -0.031 seconds) ETA: Wed Dec 2 19:57:52 2020
50%......... (T -0.025 seconds) ETA: Wed Dec 2 19:57:52 2020
60%......... (T -0.019 seconds) ETA: Wed Dec 2 19:57:52 2020
70%......... (T -0.013 seconds) ETA: Wed Dec 2 19:57:52 2020
80%......... (T -0.006 seconds) ETA: Wed Dec 2 19:57:52 2020
90%.........
Hashing NZ_GG705055.fna backwards
0%......... (T -0.058 seconds) ETA: Wed Dec 2 19:57:52 2020
10%......... (T -0.052 seconds) ETA: Wed Dec 2 19:57:52 2020
20%......... (T -0.047 seconds) ETA: Wed Dec 2 19:57:52 2020
30%......... (T -0.040 seconds) ETA: Wed Dec 2 19:57:52 2020
40%......... (T -0.034 seconds) ETA: Wed Dec 2 19:57:52 2020
50%......... (T -0.027 seconds) ETA: Wed Dec 2 19:57:52 2020
60%......... (T -0.020 seconds) ETA: Wed Dec 2 19:57:52 2020
70%......... (T -0.014 seconds) ETA: Wed Dec 2 19:57:52 2020
80%......... (T -0.007 seconds) ETA: Wed Dec 2 19:57:52 2020
90%.........
Hashing NZ_GG705055.gbk forwards
0%......... (T -0.061 seconds) ETA: Wed Dec 2 19:57:52 2020
10%......... (T -0.056 seconds) ETA: Wed Dec 2 19:57:52 2020
20%......... (T -0.049 seconds) ETA: Wed Dec 2 19:57:52 2020
30%......... (T -0.042 seconds) ETA: Wed Dec 2 19:57:52 2020
40%......... (T -0.035 seconds) ETA: Wed Dec 2 19:57:52 2020
50%......... (T -0.028 seconds) ETA: Wed Dec 2 19:57:52 2020
60%......... (T -0.021 seconds) ETA: Wed Dec 2 19:57:52 2020
70%......... (T -0.014 seconds) ETA: Wed Dec 2 19:57:52 2020
80%......... (T -0.007 seconds) ETA: Wed Dec 2 19:57:52 2020
90%.........
Hashing NZ_GG705055.gbk backwards
0%......... (T -0.061 seconds) ETA: Wed Dec 2 19:57:52 2020
10%......... (T -0.055 seconds) ETA: Wed Dec 2 19:57:52 2020
20%......... (T -0.049 seconds) ETA: Wed Dec 2 19:57:52 2020
30%......... (T -0.042 seconds) ETA: Wed Dec 2 19:57:52 2020
40%......... (T -0.035 seconds) ETA: Wed Dec 2 19:57:52 2020
50%......... (T -0.028 seconds) ETA: Wed Dec 2 19:57:52 2020
60%......... (T -0.021 seconds) ETA: Wed Dec 2 19:57:52 2020
70%......... (T -0.014 seconds) ETA: Wed Dec 2 19:57:52 2020
80%......... (T -0.007 seconds) ETA: Wed Dec 2 19:57:52 2020
90%.........
Initial hashing took: 0.276 seconds
Extracting anchors from hash-space.
(T -2.880 seconds) ETA: Wed Dec 2 19:57:55 2020
6%. (T -2.808 seconds) ETA: Wed Dec 2 19:57:56 2020
18%. (T -1.969 seconds) ETA: Wed Dec 2 19:57:55 2020
31%. (T -1.598 seconds) ETA: Wed Dec 2 19:57:55 2020
43%. (T -1.202 seconds) ETA: Wed Dec 2 19:57:55 2020
56%. (T -0.898 seconds) ETA: Wed Dec 2 19:57:55 2020
68%. (T -0.514 seconds) ETA: Wed Dec 2 19:57:55 2020
81%. (T -0.199 seconds) ETA: Wed Dec 2 19:57:55 2020
93%.
Anchor extraction completed in: 2.818 seconds
Total anchors: 0
Anchor extraction + merge time: 2.818 seconds
Total processing time: 3.364 seconds
Writing anchors...
Total seeds used in anchors: 16
Hash performance:
Keys used: 16 out of 16 possible (100.00%).
Used keyspace is 100.00% = 100.00% of magic *optimal 100.00%
Average pigeons per pigeon hole: 1
Writing 16 repeats...Output writing finished in: 0.485 seconds
Total time: 3.849 seconds
Murasaki finished!
PASSED MURASAKI
Testing Genepare on NZ_GG705055.fna
1001
PASSED GENEPARSE
Testing mbfa on NZ_GG705055.fna
/tmp/autopkgtest-lxc.razmgtoz/downtmp/build.P6A/src/debian/tests/run-unit-test:
line 17: 6660 Bus error mbfa $f --fasta > testfile
autopkgtest [19:57:56]: test run-unit-test: -----------------------]
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: murasaki
Source-Version: 1.68.6-11
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
murasaki, 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 977...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated murasaki 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: Fri, 18 Dec 2020 09:56:58 +0100
Source: murasaki
Architecture: source
Version: 1.68.6-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 977621
Changes:
murasaki (1.68.6-11) unstable; urgency=medium
.
* Skip problematic test on armhf since it results in "Bus error"
Closes: #977621
* Standards-Version: 4.5.1 (routine-update)
* Update renamed lintian tag names in lintian overrides.
* watch file standard 4 (routine-update)
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bd17b95f77022d73444f23253f0ca45525bf762d 10716 murasaki_1.68.6-11.debian.tar.xz
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murasaki_1.68.6-11_amd64.buildinfo
Checksums-Sha256:
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Files:
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9799f54f285cf5fe8ebc64861d606ef0 10716 science optional
murasaki_1.68.6-11.debian.tar.xz
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murasaki_1.68.6-11_amd64.buildinfo
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