Hi Matthias,
since a ling time libbiod does not build and it also does not
install. Current issue when trying to build it is:
...
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
Would you be able to check latest Git[1] and commit a patch that helps
building the package? I'm also wondering whether we can remove
libundead. Its in the Depends of sambaba but as far as I understood
this can go with latest libbiod (but I might be wrong).
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/libbiod
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http://fam-tille.de
