debian/changelog

-pbbam (1.0.6+dfsg-1) UNRELEASED; urgency=medium
+pbbam (1.0.6+dfsg-1) unstable; urgency=medium
 
   * Drop <!nocheck> option from python3-cram
     Closes: #934467
@@ -10,14 +10,13 @@ pbbam (1.0.6+dfsg-1) UNRELEASED; urgency=medium
     lines.
   * Remove obsolete fields Contact, Name from debian/upstream/metadata.
   * Build-Depends: cmake, libpbcopper-dev (>= 1.3.0)
+  * Adapt test results to latest samtools
+  * d-shlibs override for libpbcopper1.3.0-dev
+  * Unfortunately upstream does not distinguishe between release version
+    and SOVERSION - just follow their versioning anyway and rename
+    dynamic library package
 
-  TODO: ...  -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.1.0.6 -g -O2 -fdebug-prefix-map=/build/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbcopper -Wl,--end-group
-    FAILED: src/libpbbam.so.1.0.6 
-    c++  -o src/libpbbam.so.1.0.6 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' 'src/25a6634@@pbbam@sha/BaiIndexCache.cpp.o' 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam@sha/BamFile.cpp.o' 'src/25a6634@@pbbam@sha/BamFileMerger.cpp.o' 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' 'src/25a6634@@pbbam@sha/BamReader.cpp.o' 'src/25a6634@@pbbam@sha/BamRecord.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordView.cpp.o' 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o' 'src/25a6634@@pbbam@sha/BamWriter.cpp.o' 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o' 'src/25a6634@@pbbam@sha/BgzipFastaWriter.cpp.o' 'src/25a6634@@pbbam@sha/BgzipFastqWriter.cpp.o' 'src/25a6634@@pbbam@sha/BgzipWriter.cpp.o' 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o' 'src/25a6634@@pbbam@sha/Compare.cpp.o' 'src/25a6634@@pbbam@sha/CompositeFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/Config.cpp.o' 'src/25a6634@@pbbam@sha/DataSet.cpp.o' 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o' 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o' 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o' 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o' 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o' 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o' 'src/25a6634@@pbbam@sha/FaiIndex.cpp.o' 'src/25a6634@@pbbam@sha/FaiZmwChunker.cpp.o' 'src/25a6634@@pbbam@sha/FastaCache.cpp.o' 'src/25a6634@@pbbam@sha/FastaReader.cpp.o' 'src/25a6634@@pbbam@sha/FastaSequence.cpp.o' 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o' 'src/25a6634@@pbbam@sha/FastaWriter.cpp.o' 'src/25a6634@@pbbam@sha/FastqReader.cpp.o' 'src/25a6634@@pbbam@sha/FastqSequence.cpp.o' 'src/25a6634@@pbbam@sha/FastqWriter.cpp.o' 'src/25a6634@@pbbam@sha/FileProducer.cpp.o' 'src/25a6634@@pbbam@sha/FileUtils.cpp.o' 'src/25a6634@@pbbam@sha/FofnReader.cpp.o' 'src/25a6634@@pbbam@sha/FormatUtils.cpp.o' 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' 'src/25a6634@@pbbam@sha/IFastaWriter.cpp.o' 'src/25a6634@@pbbam@sha/IFastqWriter.cpp.o' 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastqBgzfReader.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastqReader.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastqTextReader.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastqReaderImpl.cpp.o' 'src/25a6634@@pbbam@sha/IRecordWriter.cpp.o' 'src/25a6634@@pbbam@sha/KSeqReader.cpp.o' 'src/25a6634@@pbbam@sha/MD5.cpp.o' 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o' 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o' 'src/25a6634@@pbbam@sha/PbiFile.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o' 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o' 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o' 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o' 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o' 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' 'src/25a6634@@pbbam@sha/RecordType.cpp.o' 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o' 'src/25a6634@@pbbam@sha/SamWriter.cpp.o' 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o' 'src/25a6634@@pbbam@sha/StringUtilities.cpp.o' 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o' 'src/25a6634@@pbbam@sha/Tag.cpp.o' 'src/25a6634@@pbbam@sha/TagCollection.cpp.o' 'src/25a6634@@pbbam@sha/TextFileReader.cpp.o' 'src/25a6634@@pbbam@sha/TextFileWriter.cpp.o' 'src/25a6634@@pbbam@sha/Validator.cpp.o' 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o' 'src/25a6634@@pbbam@sha/ValidationException.cpp.o' 'src/25a6634@@pbbam@sha/Version.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o' 'src/25a6634@@pbbam@sha/VirtualRegion.cpp.o' 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/XmlReader.cpp.o' 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o' 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastqReader.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastxBgzfReader.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastxReaderImpl.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastxTextReader.cpp.o' 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/bed_BedReader.cpp.o' 'src/25a6634@@pbbam@sha/bed_BedWriter.cpp.o' 'src/25a6634@@pbbam@sha/ccs_CCSPbiBuilder.cpp.o' 'src/25a6634@@pbbam@sha/ccs_CCSRecordFormat.cpp.o' 'src/25a6634@@pbbam@sha/ccs_CCSRecordReader.cpp.o' 'src/25a6634@@pbbam@sha/ccs_CCSRecordWriter.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfFile.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfHeaderTypes.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.1.0.6 -g -O2 -fdebug-prefix-map=/build/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbcopper -Wl,--end-group
-    /usr/bin/ld: cannot find -lpbcopper
-    collect2: error: ld returned 1 exit status
-
- -- Andreas Tille <tille@debian.org>  Fri, 13 Dec 2019 21:50:03 +0100
+ -- Andreas Tille <tille@debian.org>  Fri, 20 Dec 2019 11:27:03 +0100
 
 pbbam (0.23.0+dfsg-1) unstable; urgency=medium
 

debian/control

@@ -27,7 +27,7 @@ Package: pbbamtools
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libpbbam0.23.0 (= ${binary:Version})
+         libpbbam1.0.6 (= ${binary:Version})
 Recommends: samtools
 Description: processing Pacific Biosciences binary alignment/map files
  The BAM format is a binary, compressed, record-oriented container format
@@ -42,7 +42,7 @@ Description: processing Pacific Biosciences binary alignment/map files
  This package provides command-line utilities for working with PacBio BAM
  files.
 
-Package: libpbbam0.23.0
+Package: libpbbam1.0.6
 Architecture: any
 Multi-Arch: same
 Section: libs
@@ -65,7 +65,7 @@ Description: Pacific Biosciences binary alignment/map (BAM) library
 Package: libpbbam-dev
 Architecture: any
 Section: libdevel
-Depends: libpbbam0.23.0 (= ${binary:Version}),
+Depends: libpbbam1.0.6 (= ${binary:Version}),
          libhts-dev,
          libssl-dev,
          ${misc:Depends}

debian/copyright

@@ -7,7 +7,7 @@ Files-Excluded: third-party
                 */tests/scripts/cram*
 
 Files: *
-Copyright: 2014-2016 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com>
+Copyright: 2014-2019 Pacific Biosciences of California, Inc. <devnet@pacificbiosciences.com>
 License: PacBio-BSD-3-Clause
 
 Files: src/pugixml/*
@@ -15,12 +15,9 @@ Copyright: 2006-2014 Arseny Kapoulkine <arseny.kapoulkine@gmail.com>
            2003 Kristen Wegner <kristen@tima.net>
 License: MIT
 
-Files: tools/common/OptionParser.*
-Copyright: 2010 Johannes Weißl <jargon@molb.org>
-License: BSD-3-Clause or BSD-2-Clause
-
 Files: debian/*
 Copyright: 2015-2016 Afif Elghraoui <afif@debian.org>
+           2016-2019 Andreas Tille <tille@debian.org>
 License: PacBio-BSD-3-Clause
 
 License: PacBio-BSD-3-Clause
@@ -52,55 +49,6 @@ License: PacBio-BSD-3-Clause
  OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
  SUCH DAMAGE.
 
-License: BSD-3-Clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
- 2. Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
- 3. Neither the name of the University nor the names of its contributors
-    may be used to endorse or promote products derived from this software
-    without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE HOLDERS OR
- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-License: BSD-2-Clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2. Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
- WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGE.
-
 License: MIT
  Permission is hereby granted, free of charge, to any person
  obtaining a copy of this software and associated documentation

debian/patches/python3.patch

@@ -4,7 +4,7 @@ Description: Use Python3 in build time test suite
 
 --- a/meson.build
 +++ b/meson.build
-@@ -80,7 +80,7 @@ subdir('src')
+@@ -83,7 +83,7 @@ subdir('src')
  
  if not meson.is_subproject()
    if get_option('build-tools') or get_option('tests')

debian/patches/series

@@ -2,3 +2,4 @@ fix_gtest_depcheck.patch
 # debug_tests.patch
 use_debian_packaged_python3-cram.patch
 python3.patch
+results_with_latest_samtools.patch

debian/rules

@@ -56,6 +56,7 @@ override_dh_install:
 		    --exclude-la \
 		    --exclude-a \
 		    --override s/libhts2-dev/libhts-dev/ \
+		    --override s/libpbcopper1.3.0-dev/libpbcopper-dev/ \
 		    --movedev debian/tmp/usr/include/* usr/include \
 		    --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
 		    debian/tmp/usr/lib/*/*.so