[Debian-med-packaging] Bug#927166: Any chance to get libbiod compiling again?

[Andreas Tille]

On Fri, Sep 13, 2019 at 03:37:32PM +0200, Matthias Klumpp wrote:
> Am Fr., 13. Sept. 2019 um 15:21 Uhr schrieb Andreas Tille <andreas at an3as.eu>:
> > /usr/bin/ld.gold: error: bin/biod_tests.o: multiple definition of '_d_execBssBegAddr'
> > /usr/bin/ld.gold: contrib/undead/*/__main.o: previous definition here
> > /usr/bin/ld.gold: error: bin/biod_tests.o: multiple definition of '_d_execBssEndAddr'
> > /usr/bin/ld.gold: contrib/undead/*/__main.o: previous definition here
> > collect2: error: ld returned 1 exit status
> > [...]
> 
> It's very likely that undeaD needs to be updated first in order to
> compile this again.
> Has upgrading that been attempted yet?

I just upgraded libundead and re-added it to libbiod (I assumed libundead
would not have been needed for libbiod any more and thus it was removed)
Now the error is:

...
linking...
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.gold: error: bin/biod_tests.o: multiple definition of '_d_execBssBegAddr'
/usr/bin/ld.gold: contrib/undead/*/__main.o: previous definition here
/usr/bin/ld.gold: error: bin/biod_tests.o: multiple definition of '_d_execBssEndAddr'
/usr/bin/ld.gold: contrib/undead/*/__main.o: previous definition here
collect2: error: ld returned 1 exit status

Kind regards

        Andreas.


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