[Debian-med-packaging] Bug#927166: libbiod0: not installable in sid

[Andreas Tille]

On Mon, Apr 15, 2019 at 09:39:17PM +0200, Ralf Treinen wrote:
> Package: libbiod0
> Version: 0.2.1-1
> Severity: serious
> User: treinen at debia.org
                ^^^^^^^^^
@Ralf: Are you sure there is no typo in one of your scripts?

> libbiod0 is not installable on amd64 or i386 (the only architectures
> for which this binary package exists) in sid, at least since
> 2018-10-30 : it depends on libphobos2-ldc-shared81 which does 
> not exist in sid.

My guess is that this can be simply solved by a rebuild which
is fixed by a new changelog entry in Git.

@Matthias:

When I try to build the current state in Git I get:

...
ldc2 -wi -g -relocation-model=pic -unittest -main -Icontrib/undead -L-lz -O0 -d-debug -link-debuglib contrib/undead/cstream.o contrib/undead/stream.o contrib/undead/doformat.o contrib/     undead/utf.o contrib/undead/*/*.o bio/core/sequence.o bio/core/kmer.o bio/core/genotype.o bio/core/tinymap.o bio/core/base.o bio/core/decompress.o bio/core/call.o bio/core/region.o bio/    core/bgzf/inputstream.o bio/core/bgzf/constants.o bio/core/bgzf/block.o bio/core/bgzf/virtualoffset.o bio/core/bgzf/compress.o bio/core/bgzf/chunk.o bio/core/bgzf/outputstream.o bio/core/  utils/format.o bio/core/utils/exception.o bio/core/utils/outbuffer.o bio/core/utils/stream.o bio/core/utils/algo.o bio/core/utils/tmpfile.o bio/core/utils/memoize.o bio/core/utils/         switchendianness.o bio/core/utils/roundbuf.o bio/core/utils/zlib.o bio/core/utils/bylinefast.o bio/core/utils/range.o bio/std/file/fastq.o bio/std/file/fasta.o bio/std/file/fai.o bio/std/  genotype/maf.o bio/std/genotype/snp.o bio/std/range/splitter.o bio/std/sff/writer.o bio/std/sff/readrange.o bio/std/sff/index.o bio/std/sff/reader.o bio/std/sff/read.o bio/std/sff/         constants.o bio/std/maf/reader.o bio/std/maf/block.o bio/std/maf/parser.o bio/std/experimental/hts/logger.o bio/std/experimental/hts/pileup.o bio/std/experimental/hts/bgzf_writer.o bio/std/experimental/hts/reads.o bio/std/experimental/hts/bgzf.o bio/std/experimental/hts/unpack.o bio/std/experimental/hts/constants.o bio/std/experimental/hts/hashing.o bio/std/sff/utils/roundup.o bio/std/hts/iontorrent/flowcall.o bio/std/hts/iontorrent/flowindex.o bio/std/hts/sam/reader.o bio/std/hts/sam/header.o bio/std/hts/snpcallers/maq.o bio/std/hts/snpcallers/simple.o bio/   std/hts/bam/abstractreader.o bio/std/hts/bam/randomaccessmanager.o bio/std/hts/bam/baifile.o bio/std/hts/bam/writer.o bio/std/hts/bam/pileup.o bio/std/hts/bam/splitter.o bio/std/hts/bam/   tagvalue.o bio/std/hts/bam/constants.o bio/std/hts/bam/reference.o bio/std/hts/bam/baseinfo.o bio/std/hts/bam/readrange.o bio/std/hts/bam/referenceinfo.o bio/std/hts/bam/multireader.o bio/ std/hts/bam/reader.o bio/std/hts/bam/read.o bio/std/hts/bam/cigar.o bio/std/hts/bam/region.o bio/std/hts/thirdparty/msgpack.o bio/std/hts/utils/array.o bio/std/hts/utils/value.o bio/std/   hts/utils/samheadermerger.o bio/std/hts/utils/graph.o bio/std/experimental/hts/bam/reader.o bio/std/experimental/hts/bam/writer.o bio/std/experimental/hts/bam/header.o bio/std/hts/sam/     utils/recordparser.o bio/std/hts/sam/utils/fastrecordparser.o bio/std/hts/bam/md/core.o bio/std/hts/bam/md/operation.o bio/std/hts/bam/md/reconstruct.o bio/std/hts/bam/md/parse.o bio/std/  hts/bam/bai/bin.o bio/std/hts/bam/bai/indexing.o bio/std/hts/bam/validation/alignment.o bio/std/hts/bam/validation/samheader.o -of=bin/biod_tests
/usr/bin/ld: bin/biod_tests.o:(.data._d_execBssBegAddr+0x0): multiple definition of `_d_execBssBegAddr'; contrib/undead/*/__main.o:(.data._d_execBssBegAddr+0x0): first defined here
/usr/bin/ld: bin/biod_tests.o:(.data._d_execBssEndAddr+0x0): multiple definition of `_d_execBssEndAddr'; contrib/undead/*/__main.o:(.data._d_execBssEndAddr+0x0): first defined here
collect2: error: ld returned 1 exit status
Error: /usr/bin/gcc failed with status: 1


As usual I have no idea how to fix this. :-(

Kind regards

      Andreas.

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