[Debian-med-packaging] [dlang/undeaD] Meson: add meson build (#33)

[Andreas Tille]

Hi,

On Sat, Mar 16, 2019 at 09:34:21AM -0700, Matthias Klumpp wrote:
> +1 from me for just removing it from Debian. UndeaD was always a bit awkward to have anyway.

I'll ask upstream for removal once I get libbiod build again.  I confirm
that I'm more than happy to not need to maintain it any more. :-)

I now tried to build libbiod 0.2.2 using the provided Makefile (since
there is no meson.build) and was running into:


linking...
ldc2 -wi -g -relocation-model=pic -unittest -main -Icontrib/undead -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
/usr/bin/ld: bio/core/bgzf/block.o: undefined reference to symbol 'inflateEnd'
/usr/bin/ld: //lib/x86_64-linux-gnu/libz.so.1: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Error: /usr/bin/gcc failed with status: 1
make[1]: *** [Makefile:37: bin/biod_tests] Error 1
make[1]: Leaving directory '/build/libbiod-0.2.2'
dh_auto_build: make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:8: build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2


Is there any trick needed to link libz properly?
(Just commited latest packaging status to git[1])


Kind regards

       Andreas.

[1] https://salsa.debian.org/med-team/libbiod

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