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

Shayan Doust hello at shayandoust.me
Fri Jul 26 15:14:20 BST 2019


Hello Andreas,

Honestly never even heard of Dlang so I thought I'd give this a try.

I decided to disect and manually experiment with the Makefile to
understand this.

The compilation stage works well, and this is failing at the linker
stage with symbolic handling of the object files. This also tends to
happen with poor linker parameters or just some plain misconfig. I am
not sure what the main flag in DFLAGS does, but utilising the main flag
on the compiler line in Makefile and not the linker line links the
software successfully. I am not sure why a linker would need an
extensive set of flags that is the same as the compiler.

The only fault I now see with this is that it fails at the dh_install
stage, as the debian/tmp file for me is empty. I am not sure why and I
am not sure what weighing that main flag had on the linker. I decided to
manually run dub and dub test and the library unit test does run
successfully. The generated binary in the bin file also seems to invoke
without a complaint.

Those are my discoveries so far with something I've never touched
before. First bug reply so I do apologise if I did violate some reply
policy.

Best Regards,
Shayan Doust

On 16/04/2019 10:55, Andreas Tille wrote:
> 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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