On Mon, Apr 15, 2019 at 09:39:17PM +0200, Ralf Treinen wrote:
> Package: libbiod0
> Version: 0.2.1-1
> Severity: serious
> User: [email protected]
^^^^^^^^^
@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.
--
http://fam-tille.de
