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. (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.) -- 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 sequencesbt2_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 refhas 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 -qCheck that path to Bowtie2, Cutadapt, Samtools are well defined. autopkgtest [18:11:44]: test run-sample-analysisOpenPGP_signature
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--- 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) Checksums-Sha1: 0c7ebe88dc46d1d783f9dfec9639bfb94dacef64 1984 optimir_1.1-2.dsc 3f5079d84102c8d4f57d3ea111d4b6494c6ee3ef 3800 optimir_1.1-2.debian.tar.xz 59911eb29fcea6717e5a455f26736bb573fcff55 6378 optimir_1.1-2_amd64.buildinfo Checksums-Sha256: 4b0df455a9923f038cc4ac68d02eedc434dfe6dc6e0d63436e1472efef02e1a0 1984 optimir_1.1-2.dsc 683cbb8a37668a5e1faaa568c7273922c55d9d89ccc097cab792b373c00d1d30 3800 optimir_1.1-2.debian.tar.xz 0c808fa3ad259b183f00bf5e6159a88c7d582689dbce8e5d65008a261260f88c 6378 optimir_1.1-2_amd64.buildinfo Files: 54d9e7a397206ce87d2fcf808cadf5ba 1984 science optional optimir_1.1-2.dsc 87141103b7f8aa4f266c9e36bcec18c6 3800 science optional optimir_1.1-2.debian.tar.xz afa8df6d6d74be5ebb11558d9168a1f2 6378 science optional optimir_1.1-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmIptNgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFeNw/+IWQxSL4BFY/hr4og8E385wBsturD2Lf7 aQabQ03g55eolurqDckjzfKovkiKqOvTHnwvsc84gU1S7iXmXo0a42++WWkCCTHh BZiAuG6VkvfdFTcJjCTsFL6SyxHm0hc/aL8HwyLb8ujwmCQ7+zqVlrgQyilRNogv NsWjLBMxFRz+ZX2fg1laxOw+YlbQL1/QvdQt2y7WBxFPpDnsYv09kRXCZ3wxYf6E RqtKerUnf6UmKcDmi0Lb2gUP7uVhDjdsVwe1F3fsMM6sg5/qHatn6GiCR2gKtnD4 bUHbrsYJAzcH1kX441WLkIfH9KA+/S77yH3H4ZDgjw3d8lwJm+xmr6rNuoKNGpbc UOS0K7xe0AyKoMid4VeG468aRn9WKAedsHR87mldnQhAmlReNy2Wn9LSfW6L56j2 pgyQu7SLaX51IZfsvB+9XNfopslAgUJ/DcG5QvEWokxH7dtoD/5uO3YnGQ3KGEBg rlkkt/2CfqkWarVXujK3OpAnouc1WtszSYGqXSZyjAUCk3UJaNA0opQnuDCF9XRq SwDD7+1G86UwZwpuT2afqlkH6KH78hFNsMxmCmg6bEju3oAcAeDalsb0OIVvEnOK /01m/aeJVBkaVItZtWZepyYMgbKWJhNmBahSMpSgmCiP+WyGgmmsPswSZfAX2QVt zotomPx29Wc= =/mea -----END PGP SIGNATURE-----
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