Your message dated Mon, 04 Feb 2019 11:23:34 +0000
with message-id <e1gqcle-000ctc...@fasolo.debian.org>
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
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--
909071: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=909071
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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
--- End Message ---
--- 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 909...@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 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 ftpmas...@ftp-master.debian.org)
-----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
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
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
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--- End Message ---
