[Debian-med-packaging] Bug#909071: pbbam: FTBFS on every release architecture where it previously built

[Niels Thykier]

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