Bug#927166: libbiod0: not installable in sid
Hi Shayan, On Fri, Jul 26, 2019 at 03:14:20PM +0100, Shayan Doust wrote: > Honestly never even heard of Dlang so I thought I'd give this a try. Let me say at first that's quite a brave approach. I need to admit that I als never heard before I had a package which actually needs that library. > 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. I'f like to leave this suggestion for comments by Matthias Klumpp since he is the D-expert and he finally helped to get the package into the state it is now. > 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. Totally fine for reply policy - thanks a lot for your contribution Andreas. -- http://fam-tille.de
Bug#927166: libbiod0: not installable in sid
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: trei...@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 > /us
Bug#927166: libbiod0: not installable in sid
On Mon, Apr 15, 2019 at 09:39:17PM +0200, Ralf Treinen wrote: > Package: libbiod0 > Version: 0.2.1-1 > Severity: serious > User: trei...@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. -- http://fam-tille.de
Bug#927166: libbiod0: not installable in sid
Package: libbiod0 Version: 0.2.1-1 Severity: serious User: trei...@debia.org Usertags: edos-uninstallable Hi, 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. -Ralf.
