let's make it count ----- Forwarded message from Debian Bug Tracking System <owner@bugs.debian.org> ----- Date: Wed, 08 Dec 2021 20:42:05 +0000 From: Debian Bug Tracking System <owner@bugs.debian.org> To: Étienne Mollier <emollier@debian.org> Subject: Bug#1000475: marked as done (minimac4: autopkgtest regression: *** stack smashing detected ***: terminated) X-Mailer: MIME-tools 5.509 (Entity 5.509) Your message dated Wed, 08 Dec 2021 20:38:52 +0000 with message-id <E1mv3iG-000Cny-3I@fasolo.debian.org> and subject line Bug#1000475: fixed in minimac4 1.0.2-4 has caused the Debian Bug report #1000475, regarding minimac4: autopkgtest regression: *** stack smashing detected ***: terminated 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 owner@bugs.debian.org immediately.) -- 1000475: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1000475 Debian Bug Tracking System Contact owner@bugs.debian.org with problems Date: Tue, 23 Nov 2021 21:41:25 +0100 From: Paul Gevers <elbrus@debian.org> To: submit@bugs.debian.org Subject: minimac4: autopkgtest regression: *** stack smashing detected ***: terminated User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.14.0 Source: minimac4 Version: 1.0.2-3 X-Debbugs-CC: debian-ci@lists.debian.org Severity: serious User: debian-ci@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of minimac4 the autopkgtest of minimac4 fails in testing when that autopkgtest is run with the binary packages of minimac4 from unstable. It passes when run with only packages from testing. In tabular form: pass fail minimac4 from testing 1.0.2-3 all others from testing from testing I copied some of the output at the bottom of this report. Similar to bug #1000413 I think this issue points at ABI breakage. The following in the changelog looks very suspicious: * Rebuild minimac4 against new version of libstatgen This is a hint. The test passes in unstable. 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=minimac4 https://ci.debian.net/data/autopkgtest/testing/amd64/m/minimac4/16920779/log.gz -------------------------------------------------------------------------------- Minimac4 - Fast Imputation Based on State Space Reduction HMM -------------------------------------------------------------------------------- (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis Version: 1.0.2; Built: 2021-11-11 by Reproducible Command Line Options: Reference Haplotypes : --refHaps [refPanel.m3vcf.gz], --passOnly, --rsid, --referenceEstimates [ON], --mapFile [docs/geneticMapFile.b38.map.txt.gz] Target Haplotypes : --haps [targetStudy.vcf.gz] Output Parameters : --prefix [testRun], --estimate, --nobgzip, --vcfBuffer [200], --format [GT,DS], --allTypedSites, --meta, --memUsage Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00] Subset Parameters : --chr [], --start, --end, --window Approximation Parameters : --minimac3, --probThreshold [0.01], --diffThreshold [0.01], --topThreshold [0.01] Other Parameters : --log, --help, --cpus [5], --params PhoneHome : --noPhoneHome [ON], --phoneHomeThinning [50] URL = http://genome.sph.umich.edu/wiki/Minimac4 Starting Main Imputation/Estimation Analysis ... Performing preliminary check on input parameters... ------------------------------------------------------------------------------ PRELIMINARY FILE CHECK ------------------------------------------------------------------------------ Checking GWAS haplotype file : targetStudy.vcf.gz Gathering variant information ... ERROR !!! Empty Value for Individual : TA98 at First Marker Most probably a corrupted VCF file. Please check input VCF file !!! *** stack smashing detected ***: terminated Aborted autopkgtest [07:10:54]: test run-sample-analysis Date: Wed, 08 Dec 2021 20:38:52 +0000 From: Debian FTP Masters <ftpmaster@ftp-master.debian.org> To: 1000475-close@bugs.debian.org Subject: Bug#1000475: fixed in minimac4 1.0.2-4 Source: minimac4 Source-Version: 1.0.2-4 Done: Étienne Mollier <emollier@debian.org> We believe that the bug you reported is fixed in the latest version of minimac4, 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 1000475@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Étienne Mollier <emollier@debian.org> (supplier of updated minimac4 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 ftpmaster@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 08 Dec 2021 20:37:16 +0100 Source: minimac4 Architecture: source Version: 1.0.2-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Changed-By: Étienne Mollier <emollier@debian.org> Closes: 1000475 Changes: minimac4 (1.0.2-4) unstable; urgency=medium . * Team upload. * Rebuild minimac4 against libstatgen1. (Closes: #1000475) Checksums-Sha1: 9fd704e418fc359bd96c27f0d390432a16e0ec27 2012 minimac4_1.0.2-4.dsc 0c4603eba0ce09f7eccd7e132cd5d335d2573ad4 1219564 minimac4_1.0.2-4.debian.tar.xz 06f846df3a7bc4b0050f591aa2140ef2b0f3784a 6713 minimac4_1.0.2-4_amd64.buildinfo Checksums-Sha256: f2bbe1423257132fd356a4cdf3f28720bf385b0ab186d6e049d43b9c4aa192b6 2012 minimac4_1.0.2-4.dsc 3aa1634fe18173389aa4e700bcf72053f27c91d129bd55eb0ba280100c19d004 1219564 minimac4_1.0.2-4.debian.tar.xz c5f465a2dffde08662e7ef37d0b8c24b1f75ea129545a0145581e59f0e83dfc7 6713 minimac4_1.0.2-4_amd64.buildinfo Files: 63dba25947ddc643df213e48c7c7fb64 2012 science optional minimac4_1.0.2-4.dsc c694968e736ff8dae360a2523d8029d7 1219564 science optional minimac4_1.0.2-4.debian.tar.xz 949265c72d51886d9f5667bb8249bef3 6713 science optional minimac4_1.0.2-4_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmGxC0kUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdolqA//V+UJaqJ+JrLAXl6i+h4hO0GTqCYF YzxgTMjROdfRCKEEibOitgglgdW+NGbDgqxWoYmylZrs/ajKJB1cJJx6AqDWNRWF 8NxebaisPQ0Fjl2KUVnfaaz5h5Yh56nysoKEYgc8QodO+GOT4YBLHF216T3vp8aL nvGaCXhwMMdNv4gIxwdtdDrCrv7/hc0YsAekCW/xwQ1oz+RSy/xBxSV+tPFBxN1F oYrX0Kr2jY5CWF/QyFB64fnriywfPwoaCvsU2eD46+w2JvAf+VCzynaKJoozqe3c yIe5G66gdJCXGW3KeRIOA4trUdFWkqlso6VQs9Q0ghIqz7QQz9cK1OPOauvM2qjF P6dLEL6e4iBtYmEcF57/aWRJmnAX0GNeWTv+8GO2ObHvuUISIVyJFu646CD5mwZY VuWcgLoZNd+9kTWCXtie7LbSrIyXppGUbCMGrStOly0mOkBpCJo87G8PTHd35f7G gtG9Sm+T5aIhMu4zhTG72Xs/XouIR68+3SqGMwnqBdwUj/hoySkkqlbQ8+Cl71ue FLYJiF9lXkqkM7ynEmYR85EdXBgNW3RSJ2V02eN+ofWuVD+YSTOpvbfbedvycR3p ZPlZlnSj5QPvjqahp4tkdzhN7Bsl1eFbwQWo8QFOdnekTG0dZhAaufQ+MNa988HG gu8+WUDtLdA5LQo= =hyIo -----END PGP SIGNATURE----- ----- End forwarded message ----- -- Étienne Mollier <emollier@emlwks999.eu> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity.
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