Your message dated Mon, 04 Feb 2019 11:23:34 +0000 with message-id <[email protected]> and subject line Bug#909071: fixed in pbbam 0.19.0+dfsg-3 has caused the Debian Bug report #909071, regarding pbbam: FTBFS on every release architecture where it previously built 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 [email protected] immediately.) -- 909071: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=909071 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: pbbam Version: 0.18.0+dfsg-1 Severity: serious Hi, The pbbam package FTBFS on every release architecture. The following snippet is from the arm64 build: """ # Fix broken PATH synthetic_movie_all_path=`find $PWD -name synthetic_movie_all.subreadset.xml` ; \ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${synthetic_movie_all_path}?" tests/src/cram/pbbamify* BINDIR=`dirname $(find $PWD -name pbmerge -type f -executable)`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \ cram -v tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbbamify.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t: failed --- tests/src/cram/pbmerge_pacbio_ordering.deb.t +++ tests/src/cram/pbmerge_pacbio_ordering.deb.t.err @@ -14,444 +14,104 @@ Sanity Check: $ samtools view -H $HQREGION_BAM - @HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc) - @RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc) - @PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc) - @PG\tID:bazFormat-0.3.0\tPN:bazFormat\tVN:0.3.0 (esc) - @PG\tID:bazwriter-0.15.0\tPN:bazwriter\tVN:0.15.0 (esc) + [E::hts_open_format] Failed to open file /<<BUILDDIR>>/pbbam-0.18.0/tests/data/polymerase/internal.hqregions.bam + samtools view: failed to open "/<<BUILDDIR>>/pbbam-0.18.0/tests/data/polymerase/internal.hqregions.bam" for reading: No such file or directory + [1] $ samtools view $HQREGION_BAM | cut -f 1 - ArminsFakeMovie/100000/2659_7034 + [E::hts_open_format] Failed to open file /<<BUILDDIR>>/pbbam-0.18.0/tests/data/polymerase/internal.hqregions.bam + samtools view: failed to open "/<<BUILDDIR>>/pbbam-0.18.0/tests/data/polymerase/internal.hqregions.bam" for reading: No such file or directory [...] """ Thanks, ~Niels
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--- Begin Message ---Source: pbbam Source-Version: 0.19.0+dfsg-3 We believe that the bug you reported is fixed in the latest version of pbbam, 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated pbbam 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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 04 Feb 2019 11:50:20 +0100 Source: pbbam Binary: pbbamtools libpbbam0.19.0 libpbbam-dev Architecture: source Version: 0.19.0+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers) libpbbam0.19.0 - Pacific Biosciences binary alignment/map (BAM) library pbbamtools - processing Pacific Biosciences binary alignment/map files Closes: 909071 Changes: pbbam (0.19.0+dfsg-3) unstable; urgency=medium . * Team upload. . [ Steve Langasek ] * Fix build dir name for tests Closes: #909071 Checksums-Sha1: b940ff1dbb072b37efa5a51268a9ca16ccdcb833 2304 pbbam_0.19.0+dfsg-3.dsc 5fe73e3a2c680540769b762f8750ad1a6bdac088 7124 pbbam_0.19.0+dfsg-3.debian.tar.xz 64248c4f0b9ebbce20a5852ff6996c98166bf99a 14679 pbbam_0.19.0+dfsg-3_source.buildinfo Checksums-Sha256: b169c64c0ad54bc6f9768aead6f15b5894806e8a988ea9dd96a2ec205bd37a63 2304 pbbam_0.19.0+dfsg-3.dsc e88d2514e70a6b33ba06868bb7beba241290b417ec631628cde7c049b4771300 7124 pbbam_0.19.0+dfsg-3.debian.tar.xz 9d9989d17fe5d356400ddd75917917e8eec784c667fccf6ebe2a3c40263df845 14679 pbbam_0.19.0+dfsg-3_source.buildinfo Files: 3d356dd29014b5206175ccc6a1c3be85 2304 science optional pbbam_0.19.0+dfsg-3.dsc 8fe584d10bc782d4d90052ee73ce0fd3 7124 science optional pbbam_0.19.0+dfsg-3.debian.tar.xz af6bc34292f82455f262a4ca641478e7 14679 science optional pbbam_0.19.0+dfsg-3_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJCBAEBCAAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxYG/wOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtHKsA//SN8zm4bKv0H6Hm+yWj4/YHvF799fpVU9+re7 mDub0YDguJmYLrDhl43uJb7CcQkPyTI42WyWJ29TJU/JUKvkAa7XrYY3TsLJwEks BnpV+1cHUjny0y841ZbUwgS/cXRG/FTJLfiZTZqIUH05c0kjL5OqbJWUi8pnP9lS ogOtKhlgU3D6YLb+dorkNVuaqX05dG6HkCoKjZSjyChowpn88E5iz+j+DFiWLe6i htDGAaNcY5Uz3e94g8WzIBQ+aVFGzk43YKY7zrkRhuj69XmRXwltuGino7xUZ2nl RBtGpMI4vvVlG+pLz5UuAZPiq7//kWVM7oW3lWQnDSNH4FvoTWElF8M7dLCeYhnY cMZsJVMgLr7hwmwTQy4Ax/Rc7LGEpPeuNxnwzLN3ZQoaGEf4oPjbJVHjSc1MAU4X zrGKqHFpSpWjUO0rv3rE2F/NzePFwsAYV1zgDTsTASgqGNf/7Qvadby4FK6XVRzK etTgs2V5bY/fNXQLArXE+Z+8g2vVrhsGVtjLXpMpvQSvRblHWirmkItSsW/jE8E9 2zcogu9IZnGjp07z/O7nQYY/9mDFZsixELppgofm+oLftoKBLghkxQrUGHs/gYsM /ZdbSJExrVrgTZbQOzt7QZqcR6YLtVu0MQg0Bo+WwMUGWaLBf+Bozo9zBESlIh/u jsxzTmE= =CEtX -----END PGP SIGNATURE-----
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