Your message dated Tue, 28 Aug 2018 14:10:47 +0000 with message-id <e1fuehj-000fh2...@fasolo.debian.org> and subject line Bug#906980: fixed in kmer 0~20150903+r2013-6 has caused the Debian Bug report #906980, regarding kmer: autopkgtest fails with segfault in testing/unstable while it passes in stable 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.) -- 906980: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=906980 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: kmer Version: 0~20150903+r2013-4 Severity: serious Justification: reproducibility An autopkgtest fails with segfault in testing and unstable [1]. ``` /usr/bin/../lib/atac/bin/statsGenerator -a /tmp/autopkgtest-lxc.epng5fx9/downtmp/autopkgtest_tmp/results/EcolivsSent.atac -p /tmp/autopkgtest-lxc.epng5fx9/downtmp/autopkgtest_tmp/results/stats/EcolivsSent -g A > /tmp/autopkgtest-lxc.epng5fx9/downtmp/autopkgtest_tmp/results/stats/EcolivsSent.stats Segmentation fault Failed to ganerate statistics. ``` Notably, that building and testing in stable were successful (I tested it in clean chroot). JFI, I tried installing an older version of gcc on testing, the one that is used in stable (4:6.3.0-4), and this eliminated the segfault. [1] https://ci.debian.net/packages/k/kmer/ -- System Information: Debian Release: buster/sid APT prefers testing APT policy: (500, 'testing'), (50, 'unstable') Architecture: amd64 (x86_64) Kernel: Linux 4.16.0-2-amd64 (SMP w/2 CPU cores) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled
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--- Begin Message ---Source: kmer Source-Version: 0~20150903+r2013-6 We believe that the bug you reported is fixed in the latest version of kmer, 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 906...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Liubov Chuprikova <chuprikov...@gmail.com> (supplier of updated kmer 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: Mon, 27 Aug 2018 11:37:43 +0200 Source: kmer Binary: kmer libkmer-dev meryl libmeryl-dev leaff sim4db atac kmer-examples Architecture: source amd64 all Version: 0~20150903+r2013-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Liubov Chuprikova <chuprikov...@gmail.com> Description: atac - genome assembly-to-assembly comparison kmer - suite of tools for DNA sequence analysis kmer-examples - sample data for kmer suite of tools for DNA sequence analysis leaff - biological sequence library utilities and applications libkmer-dev - suite of tools for DNA sequence analysis (development lib) libmeryl-dev - in- and out-of-core kmer counting and utilities (development lib) meryl - in- and out-of-core kmer counting and utilities sim4db - batch spliced alignment of cDNA sequences to a target genome Closes: 906980 Changes: kmer (0~20150903+r2013-6) unstable; urgency=medium . * Team upload. . [ Liubov Chuprikova ] * Add autopkgtest. * Standards-Version: 4.2.1 * Add a patch to fix wrong evaluation order in an expression Closes: #906980 . 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