Your message dated Thu, 10 Mar 2022 08:34:25 +0000
with message-id <e1nsefd-0006tq...@fasolo.debian.org>
and subject line Bug#1006657: fixed in optimir 1.1-2
has caused the Debian Bug report #1006657,
regarding bowtie2 breaks optimir autopkgtest: Error with system call: Bowtie2
index creation failed
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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--
1006657: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1006657
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: bowtie2, optimir
Control: found -1 bowtie2/2.4.5-1
Control: found -1 optimir/1.1-1
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of bowtie2 the autopkgtest of optimir fails in
testing when that autopkgtest is run with the binary packages of bowtie2
from unstable. It passes when run with only packages from testing. In
tabular form:
pass fail
bowtie2 from testing 2.4.5-1
optimir from testing 1.1-1
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 of bowtie2 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=bowtie2
https://ci.debian.net/data/autopkgtest/testing/amd64/o/optimir/19635699/log.gz
No output file specified!
Bowtie 2 version 2.4.5 by Ben Langmead (lang...@cs.jhu.edu,
www.cs.jhu.edu/~langmea)
Usage: bowtie2-build [options]* <reference_in> <bt2_index_base>
reference_in comma-separated list of files with ref
sequences
bt2_index_base write bt2 data to files with this dir/basename
*** Bowtie 2 indexes will work with Bowtie v1.2.3 and later. ***
Options:
-f reference files are Fasta (default)
-c reference sequences given on cmd line (as
<reference_in>)
--large-index force generated index to be 'large', even
if ref
has fewer than 4 billion nucleotides
--debug use the debug binary; slower, assertions
enabled
--verbose log the issued command
-a/--noauto disable automatic -p/--bmax/--dcv
memory-fitting
-p/--packed use packed strings internally; slower, less
memory
--bmax <int> max bucket sz for blockwise suffix-array
builder
--bmaxdivn <int> max bucket sz as divisor of ref len
(default: 4)
--dcv <int> diff-cover period for blockwise (default: 1024)
--nodc disable diff-cover (algorithm becomes
quadratic)
-r/--noref don't build .3/.4 index files
-3/--justref just build .3/.4 index files
-o/--offrate <int> SA is sampled every 2^<int> BWT chars
(default: 5)
-t/--ftabchars <int> # of chars consumed in initial lookup
(default: 10)
--threads <int> # of threads
--seed <int> seed for random number generator
-q/--quiet verbose output (for debugging)
--h/--help print this message and quit
--version print version information and quit
#########################
## OPTIMIR ##
#########################
Starting workflow for sample S1
> Starting Library preparation...
Error with system call: Bowtie2 index creation failed: command line =
bowtie2-build -f
/tmp/autopkgtest-lxc.ej3c3g68/downtmp/autopkgtest_tmp/OptimiR_Results_Dir/OptimiR_lib/fasta/optimiR_library.fa
/tmp/autopkgtest-lxc.ej3c3g68/downtmp/autopkgtest_tmp/OptimiR_Results_Dir/OptimiR_lib/bowtie2_index/optimiR_alignment_library
-q
Check that path to Bowtie2, Cutadapt, Samtools are well defined.
autopkgtest [18:11:44]: test run-sample-analysis
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: optimir
Source-Version: 1.1-2
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
optimir, 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 1006...@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 optimir 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: SHA512
Format: 1.8
Date: Thu, 10 Mar 2022 09:14:48 +0100
Source: optimir
Architecture: source
Version: 1.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1006657
Changes:
optimir (1.1-2) unstable; urgency=medium
.
* Team upload.
* Use default name for autopkgtest and install it into docs
* Fix sequence of options in bowtie2 call
Closes: #1006657
* Standards-Version: 4.6.0 (routine-update)
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--- End Message ---
