[Debian-med-packaging] Bug#917721: libbiod: FTBFS: dh_auto_test: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 MESON_TESTTHREADS=2 ninja test returned exit code 1
Andreas Tille
tille at debian.org
Thu Jan 10 07:48:44 GMT 2019
Control: forwarded -1 https://github.com/biod/BioD/issues/50
Control: tags -1 help upstream
Dear Matthias,
unfortunately there is another issue with libbiod and as usual I need
your help due to my total incompetence in D. :-(
I have reported the issue upstream as well.
Kind regards
Andreas.
On Sat, Dec 29, 2018 at 11:06:47PM +0100, Lucas Nussbaum wrote:
> Source: libbiod
> Version: 0.2.1-1
> Severity: serious
> Justification: FTBFS on amd64
> Tags: buster sid
> Usertags: ftbfs-20181229 ftbfs-buster
>
> Hi,
>
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
>
> Relevant part (hopefully):
> > debian/rules build
> > dpkg-query: no packages found matching gdc
> > dh build
> > dh_update_autotools_config
> > dh_autoreconf
> > dh_auto_configure
> > cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu --libexecdir=lib/x86_64-linux-gnu
> > The Meson build system
> > Version: 0.49.0
> > Source dir: /<<PKGBUILDDIR>>
> > Build dir: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
> > Build type: native build
> > Project name: BioD
> > Project version: 0.2.2
> > Appending DFLAGS from environment: '-O -g -release -wi'
> > Appending LDFLAGS from environment: '-Wl,-z,relro -Wl,-z,now'
> > Native D compiler: ldc2 (llvm 1.12.0 "LDC - the LLVM D compiler (1.12.0):")
> > Build machine cpu family: x86_64
> > Build machine cpu: x86_64
> > Found pkg-config: /usr/bin/pkg-config (0.29)
> > Dependency undead found: YES 1.0.7
> > Dependency zlib found: YES 1.2.11
> > Build targets in project: 2
> > Found ninja-1.8.2 at /usr/bin/ninja
> > dh_auto_build
> > cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j2 -v
> > [1/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_bai_bin.d.o' -c ../bio/bam/bai/bin.d
> > [2/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_abstractreader.d.o' -c ../bio/bam/abstractreader.d
> > [3/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_baifile.d.o' -c ../bio/bam/baifile.d
> > [4/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_baseinfo.d.o' -c ../bio/bam/baseinfo.d
> > [5/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_cigar.d.o' -c ../bio/bam/cigar.d
> > [6/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_constants.d.o' -c ../bio/bam/constants.d
> > [7/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_bai_indexing.d.o' -c ../bio/bam/bai/indexing.d
> > [8/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_iontorrent_flowindex.d.o' -c ../bio/bam/iontorrent/flowindex.d
> > [9/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_md_core.d.o' -c ../bio/bam/md/core.d
> > [10/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_iontorrent_flowcall.d.o' -c ../bio/bam/iontorrent/flowcall.d
> > [11/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_md_operation.d.o' -c ../bio/bam/md/operation.d
> > [12/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_md_reconstruct.d.o' -c ../bio/bam/md/reconstruct.d
> > [13/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_md_parse.d.o' -c ../bio/bam/md/parse.d
> > [14/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_pileup.d.o' -c ../bio/bam/pileup.d
> > [15/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_randomaccessmanager.d.o' -c ../bio/bam/randomaccessmanager.d
> > [16/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_multireader.d.o' -c ../bio/bam/multireader.d
> > [17/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_read.d.o' -c ../bio/bam/read.d
> > [18/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_readrange.d.o' -c ../bio/bam/readrange.d
> > [19/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_reader.d.o' -c ../bio/bam/reader.d
> > [20/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_referenceinfo.d.o' -c ../bio/bam/referenceinfo.d
> > [21/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_region.d.o' -c ../bio/bam/region.d
> > [22/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_reference.d.o' -c ../bio/bam/reference.d
> > [23/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_snpcallers_simple.d.o' -c ../bio/bam/snpcallers/simple.d
> > [24/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_snpcallers_maq.d.o' -c ../bio/bam/snpcallers/maq.d
> > [25/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_splitter.d.o' -c ../bio/bam/splitter.d
> > [26/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_thirdparty_msgpack.d.o' -c ../bio/bam/thirdparty/msgpack.d
> > [27/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_utils_array.d.o' -c ../bio/bam/utils/array.d
> > [28/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_utils_graph.d.o' -c ../bio/bam/utils/graph.d
> > [29/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_tagvalue.d.o' -c ../bio/bam/tagvalue.d
> > [30/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_utils_value.d.o' -c ../bio/bam/utils/value.d
> > [31/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_utils_samheadermerger.d.o' -c ../bio/bam/utils/samheadermerger.d
> > [32/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_validation_samheader.d.o' -c ../bio/bam/validation/samheader.d
> > [33/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_writer.d.o' -c ../bio/bam/writer.d
> > [34/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_base.d.o' -c ../bio/core/base.d
> > [35/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_bgzf_block.d.o' -c ../bio/core/bgzf/block.d
> > [36/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_bgzf_chunk.d.o' -c ../bio/core/bgzf/chunk.d
> > [37/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_bgzf_compress.d.o' -c ../bio/core/bgzf/compress.d
> > [38/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_bgzf_constants.d.o' -c ../bio/core/bgzf/constants.d
> > [39/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_logger.d.o' -c ../bio2/logger.d
> > [40/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_bgzf_inputstream.d.o' -c ../bio/core/bgzf/inputstream.d
> > [41/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_bam_validation_alignment.d.o' -c ../bio/bam/validation/alignment.d
> > [42/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_bgzf_virtualoffset.d.o' -c ../bio/core/bgzf/virtualoffset.d
> > [43/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_bgzf_outputstream.d.o' -c ../bio/core/bgzf/outputstream.d
> > [44/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_call.d.o' -c ../bio/core/call.d
> > [45/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_fastq.d.o' -c ../bio/core/fastq.d
> > [46/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_genotype.d.o' -c ../bio/core/genotype.d
> > [47/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_fasta.d.o' -c ../bio/core/fasta.d
> > [48/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_kmer.d.o' -c ../bio/core/kmer.d
> > [49/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_region.d.o' -c ../bio/core/region.d
> > [50/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_tinymap.d.o' -c ../bio/core/tinymap.d
> > [51/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_algo.d.o' -c ../bio/core/utils/algo.d
> > [52/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_sequence.d.o' -c ../bio/core/sequence.d
> > [53/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_exception.d.o' -c ../bio/core/utils/exception.d
> > [54/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_format.d.o' -c ../bio/core/utils/format.d
> > [55/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_memoize.d.o' -c ../bio/core/utils/memoize.d
> > [56/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_bylinefast.d.o' -c ../bio/core/utils/bylinefast.d
> > [57/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_outbuffer.d.o' -c ../bio/core/utils/outbuffer.d
> > [58/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_range.d.o' -c ../bio/core/utils/range.d
> > [59/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_roundbuf.d.o' -c ../bio/core/utils/roundbuf.d
> > [60/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_switchendianness.d.o' -c ../bio/core/utils/switchendianness.d
> > [61/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_stream.d.o' -c ../bio/core/utils/stream.d
> > [62/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_tmpfile.d.o' -c ../bio/core/utils/tmpfile.d
> > [63/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_core_utils_zlib.d.o' -c ../bio/core/utils/zlib.d
> > [64/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_maf_block.d.o' -c ../bio/maf/block.d
> > [65/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_maf_reader.d.o' -c ../bio/maf/reader.d
> > [66/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_maf_parser.d.o' -c ../bio/maf/parser.d
> > [67/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sam_reader.d.o' -c ../bio/sam/reader.d
> > [68/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sam_header.d.o' -c ../bio/sam/header.d
> > [69/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sam_utils_recordparser.d.o' -c ../bio/sam/utils/recordparser.d
> > sam_alignment.rl(51): Warning: statement is not reachable
> > sam_alignment.rl(52): Warning: statement is not reachable
> > sam_alignment.rl(59): Warning: statement is not reachable
> > sam_alignment.rl(60): Warning: statement is not reachable
> > sam_alignment.rl(68): Warning: statement is not reachable
> > sam_alignment.rl(69): Warning: statement is not reachable
> > sam_alignment.rl(76): Warning: statement is not reachable
> > sam_alignment.rl(77): Warning: statement is not reachable
> > sam_alignment.rl(82): Warning: statement is not reachable
> > sam_alignment.rl(83): Warning: statement is not reachable
> > sam_alignment.rl(131): Warning: statement is not reachable
> > sam_alignment.rl(132): Warning: statement is not reachable
> > sam_alignment.rl(163): Warning: statement is not reachable
> > sam_alignment.rl(164): Warning: statement is not reachable
> > sam_alignment.rl(176): Warning: statement is not reachable
> > sam_alignment.rl(177): Warning: statement is not reachable
> > sam_alignment.rl(188): Warning: statement is not reachable
> > sam_alignment.rl(189): Warning: statement is not reachable
> > sam_alignment.rl(221): Warning: statement is not reachable
> > sam_alignment.rl(222): Warning: statement is not reachable
> > sam_alignment.rl(250): Warning: statement is not reachable
> > sam_alignment.rl(252): Warning: statement is not reachable
> > sam_alignment.rl(407): Warning: statement is not reachable
> > sam_alignment.rl(409): Warning: statement is not reachable
> > sam_alignment.rl(51): Warning: statement is not reachable
> > sam_alignment.rl(59): Warning: statement is not reachable
> > sam_alignment.rl(68): Warning: statement is not reachable
> > sam_alignment.rl(76): Warning: statement is not reachable
> > sam_alignment.rl(82): Warning: statement is not reachable
> > sam_alignment.rl(131): Warning: statement is not reachable
> > sam_alignment.rl(163): Warning: statement is not reachable
> > sam_alignment.rl(176): Warning: statement is not reachable
> > sam_alignment.rl(188): Warning: statement is not reachable
> > sam_alignment.rl(221): Warning: statement is not reachable
> > sam_alignment.rl(250): Warning: statement is not reachable
> > sam_alignment.rl(407): Warning: statement is not reachable
> > [70/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sff_constants.d.o' -c ../bio/sff/constants.d
> > [71/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sff_index.d.o' -c ../bio/sff/index.d
> > [72/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sff_read.d.o' -c ../bio/sff/read.d
> > [73/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sam_utils_fastrecordparser.d.o' -c ../bio/sam/utils/fastrecordparser.d
> > sam_alignment.rl(51): Warning: statement is not reachable
> > sam_alignment.rl(59): Warning: statement is not reachable
> > sam_alignment.rl(68): Warning: statement is not reachable
> > sam_alignment.rl(76): Warning: statement is not reachable
> > sam_alignment.rl(82): Warning: statement is not reachable
> > sam_alignment.rl(131): Warning: statement is not reachable
> > sam_alignment.rl(163): Warning: statement is not reachable
> > sam_alignment.rl(176): Warning: statement is not reachable
> > sam_alignment.rl(188): Warning: statement is not reachable
> > sam_alignment.rl(221): Warning: statement is not reachable
> > sam_alignment.rl(250): Warning: statement is not reachable
> > sam_alignment.rl(407): Warning: statement is not reachable
> > sam_alignment.rl(52): Warning: statement is not reachable
> > sam_alignment.rl(60): Warning: statement is not reachable
> > sam_alignment.rl(69): Warning: statement is not reachable
> > sam_alignment.rl(77): Warning: statement is not reachable
> > sam_alignment.rl(83): Warning: statement is not reachable
> > sam_alignment.rl(132): Warning: statement is not reachable
> > sam_alignment.rl(164): Warning: statement is not reachable
> > sam_alignment.rl(177): Warning: statement is not reachable
> > sam_alignment.rl(189): Warning: statement is not reachable
> > sam_alignment.rl(222): Warning: statement is not reachable
> > sam_alignment.rl(252): Warning: statement is not reachable
> > sam_alignment.rl(409): Warning: statement is not reachable
> > sam_alignment.rl(51): Warning: statement is not reachable
> > sam_alignment.rl(59): Warning: statement is not reachable
> > sam_alignment.rl(68): Warning: statement is not reachable
> > sam_alignment.rl(76): Warning: statement is not reachable
> > sam_alignment.rl(82): Warning: statement is not reachable
> > sam_alignment.rl(131): Warning: statement is not reachable
> > sam_alignment.rl(163): Warning: statement is not reachable
> > sam_alignment.rl(176): Warning: statement is not reachable
> > sam_alignment.rl(188): Warning: statement is not reachable
> > sam_alignment.rl(221): Warning: statement is not reachable
> > sam_alignment.rl(250): Warning: statement is not reachable
> > sam_alignment.rl(407): Warning: statement is not reachable
> > [74/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sff_reader.d.o' -c ../bio/sff/reader.d
> > [75/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sff_readrange.d.o' -c ../bio/sff/readrange.d
> > [76/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sff_utils_roundup.d.o' -c ../bio/sff/utils/roundup.d
> > [77/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio_sff_writer.d.o' -c ../bio/sff/writer.d
> > [78/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_bam_header.d.o' -c ../bio2/bam/header.d
> > [79/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_bam_writer.d.o' -c ../bio2/bam/writer.d
> > [80/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_bam_reader.d.o' -c ../bio2/bam/reader.d
> > [81/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_bgzf.d.o' -c ../bio2/bgzf.d
> > [82/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_constants.d.o' -c ../bio2/constants.d
> > [83/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_hashing.d.o' -c ../bio2/hashing.d
> > [84/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_pileup.d.o' -c ../bio2/pileup.d
> > [85/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_reads.d.o' -c ../bio2/reads.d
> > [86/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_bgzf_writer.d.o' -c ../bio2/bgzf_writer.d
> > [87/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_bgzf_constants.d.o' -c ../bio/core/bgzf/constants.d
> > [88/177] ldc2 -I=biod at sha -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -relocation-model=pic -of='biod at sha/bio2_unpack.d.o' -c ../bio2/unpack.d
> > [89/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_bgzf_virtualoffset.d.o' -c ../bio/core/bgzf/virtualoffset.d
> > [90/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_bgzf_outputstream.d.o' -c ../bio/core/bgzf/outputstream.d
> > [91/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_bgzf_inputstream.d.o' -c ../bio/core/bgzf/inputstream.d
> > [92/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_abstractreader.d.o' -c ../bio/bam/abstractreader.d
> > [93/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_bai_bin.d.o' -c ../bio/bam/bai/bin.d
> > [94/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_baifile.d.o' -c ../bio/bam/baifile.d
> > [95/177] ldc2 -of=libbiod.so.0.2.2 'biod at sha/bio_bam_abstractreader.d.o' 'biod at sha/bio_bam_bai_bin.d.o' 'biod at sha/bio_bam_baifile.d.o' 'biod at sha/bio_bam_bai_indexing.d.o' 'biod at sha/bio_bam_baseinfo.d.o' 'biod at sha/bio_bam_cigar.d.o' 'biod at sha/bio_bam_constants.d.o' 'biod at sha/bio_bam_iontorrent_flowcall.d.o' 'biod at sha/bio_bam_iontorrent_flowindex.d.o' 'biod at sha/bio_bam_md_core.d.o' 'biod at sha/bio_bam_md_operation.d.o' 'biod at sha/bio_bam_md_parse.d.o' 'biod at sha/bio_bam_md_reconstruct.d.o' 'biod at sha/bio_bam_multireader.d.o' 'biod at sha/bio_bam_pileup.d.o' 'biod at sha/bio_bam_randomaccessmanager.d.o' 'biod at sha/bio_bam_read.d.o' 'biod at sha/bio_bam_reader.d.o' 'biod at sha/bio_bam_readrange.d.o' 'biod at sha/bio_bam_reference.d.o' 'biod at sha/bio_bam_referenceinfo.d.o' 'biod at sha/bio_bam_region.d.o' 'biod at sha/bio_bam_snpcallers_maq.d.o' 'biod at sha/bio_bam_snpcallers_simple.d.o' 'biod at sha/bio_bam_splitter.d.o' 'biod at sha/bio_bam_tagvalue.d.o' 'biod at sha/bio_bam_thirdparty_msgpack.d.o' 'biod at sha/bio_bam_utils_array.d.o' 'biod at sha/bio_bam_utils_graph.d.o' 'biod at sha/bio_bam_utils_samheadermerger.d.o' 'biod at sha/bio_bam_utils_value.d.o' 'biod at sha/bio_bam_validation_alignment.d.o' 'biod at sha/bio_bam_validation_samheader.d.o' 'biod at sha/bio_bam_writer.d.o' 'biod at sha/bio_core_base.d.o' 'biod at sha/bio_core_bgzf_block.d.o' 'biod at sha/bio_core_bgzf_chunk.d.o' 'biod at sha/bio_core_bgzf_compress.d.o' 'biod at sha/bio_core_bgzf_constants.d.o' 'biod at sha/bio_core_bgzf_inputstream.d.o' 'biod at sha/bio_core_bgzf_outputstream.d.o' 'biod at sha/bio_core_bgzf_virtualoffset.d.o' 'biod at sha/bio_core_call.d.o' 'biod at sha/bio_core_fasta.d.o' 'biod at sha/bio_core_fastq.d.o' 'biod at sha/bio_core_genotype.d.o' 'biod at sha/bio_core_kmer.d.o' 'biod at sha/bio_core_region.d.o' 'biod at sha/bio_core_sequence.d.o' 'biod at sha/bio_core_tinymap.d.o' 'biod at sha/bio_core_utils_algo.d.o' 'biod at sha/bio_core_utils_bylinefast.d.o' 'biod at sha/bio_core_utils_exception.d.o' 'biod at sha/bio_core_utils_format.d.o' 'biod at sha/bio_core_utils_memoize.d.o' 'biod at sha/bio_core_utils_outbuffer.d.o' 'biod at sha/bio_core_utils_range.d.o' 'biod at sha/bio_core_utils_roundbuf.d.o' 'biod at sha/bio_core_utils_stream.d.o' 'biod at sha/bio_core_utils_switchendianness.d.o' 'biod at sha/bio_core_utils_tmpfile.d.o' 'biod at sha/bio_core_utils_zlib.d.o' 'biod at sha/bio_maf_block.d.o' 'biod at sha/bio_maf_parser.d.o' 'biod at sha/bio_maf_reader.d.o' 'biod at sha/bio_sam_header.d.o' 'biod at sha/bio_sam_reader.d.o' 'biod at sha/bio_sam_utils_fastrecordparser.d.o' 'biod at sha/bio_sam_utils_recordparser.d.o' 'biod at sha/bio_sff_constants.d.o' 'biod at sha/bio_sff_index.d.o' 'biod at sha/bio_sff_read.d.o' 'biod at sha/bio_sff_reader.d.o' 'biod at sha/bio_sff_readrange.d.o' 'biod at sha/bio_sff_utils_roundup.d.o' 'biod at sha/bio_sff_writer.d.o' 'biod at sha/bio2_bam_header.d.o' 'biod at sha/bio2_bam_reader.d.o' 'biod at sha/bio2_bam_writer.d.o' 'biod at sha/bio2_bgzf.d.o' 'biod at sha/bio2_bgzf_writer.d.o' 'biod at sha/bio2_constants.d.o' 'biod at sha/bio2_hashing.d.o' 'biod at sha/bio2_logger.d.o' 'biod at sha/bio2_pileup.d.o' 'biod at sha/bio2_reads.d.o' 'biod at sha/bio2_unpack.d.o' -shared -relocation-model=pic -L=-soname -L=libbiod.so.0 -O -g -release -wi -L=-z -L=relro -L=-z -L=now -L=-lundead -L=-lz
> > [96/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_bai_indexing.d.o' -c ../bio/bam/bai/indexing.d
> > [97/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_baseinfo.d.o' -c ../bio/bam/baseinfo.d
> > [98/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_cigar.d.o' -c ../bio/bam/cigar.d
> > [99/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_constants.d.o' -c ../bio/bam/constants.d
> > [100/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_iontorrent_flowcall.d.o' -c ../bio/bam/iontorrent/flowcall.d
> > [101/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_iontorrent_flowindex.d.o' -c ../bio/bam/iontorrent/flowindex.d
> > [102/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_md_core.d.o' -c ../bio/bam/md/core.d
> > [103/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/test_unittests.d.o' -c ../test/unittests.d
> > [104/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_md_operation.d.o' -c ../bio/bam/md/operation.d
> > [105/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_md_parse.d.o' -c ../bio/bam/md/parse.d
> > [106/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_md_reconstruct.d.o' -c ../bio/bam/md/reconstruct.d
> > [107/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_multireader.d.o' -c ../bio/bam/multireader.d
> > [108/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_pileup.d.o' -c ../bio/bam/pileup.d
> > [109/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_randomaccessmanager.d.o' -c ../bio/bam/randomaccessmanager.d
> > [110/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_read.d.o' -c ../bio/bam/read.d
> > [111/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_readrange.d.o' -c ../bio/bam/readrange.d
> > [112/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_reader.d.o' -c ../bio/bam/reader.d
> > [113/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_reference.d.o' -c ../bio/bam/reference.d
> > [114/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_region.d.o' -c ../bio/bam/region.d
> > [115/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_referenceinfo.d.o' -c ../bio/bam/referenceinfo.d
> > [116/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_snpcallers_simple.d.o' -c ../bio/bam/snpcallers/simple.d
> > [117/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_snpcallers_maq.d.o' -c ../bio/bam/snpcallers/maq.d
> > [118/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_splitter.d.o' -c ../bio/bam/splitter.d
> > [119/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_tagvalue.d.o' -c ../bio/bam/tagvalue.d
> > [120/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_utils_array.d.o' -c ../bio/bam/utils/array.d
> > [121/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_utils_graph.d.o' -c ../bio/bam/utils/graph.d
> > [122/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_thirdparty_msgpack.d.o' -c ../bio/bam/thirdparty/msgpack.d
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion not done for `-header`, use '-transition=intpromote' switch or `-cast(int)(header)`
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion not done for `-header`, use '-transition=intpromote' switch or `-cast(int)(header)`
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion not done for `-cast(byte)-header`, use '-transition=intpromote' switch or `-cast(int)(cast(byte)-header)`
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion not done for `-header`, use '-transition=intpromote' switch or `-cast(int)(header)`
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion not done for `-cast(short)-header`, use '-transition=intpromote' switch or `-cast(int)(cast(short)-header)`
> > ../bio/bam/thirdparty/msgpack.d(2035): Deprecation: integral promotion not done for `-header`, use '-transition=intpromote' switch or `-cast(int)(header)`
> > [123/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_utils_value.d.o' -c ../bio/bam/utils/value.d
> > [124/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_utils_samheadermerger.d.o' -c ../bio/bam/utils/samheadermerger.d
> > [125/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_validation_samheader.d.o' -c ../bio/bam/validation/samheader.d
> > [126/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_writer.d.o' -c ../bio/bam/writer.d
> > [127/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_base.d.o' -c ../bio/core/base.d
> > [128/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_bgzf_block.d.o' -c ../bio/core/bgzf/block.d
> > [129/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_bgzf_chunk.d.o' -c ../bio/core/bgzf/chunk.d
> > [130/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_bam_validation_alignment.d.o' -c ../bio/bam/validation/alignment.d
> > [131/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_bgzf_compress.d.o' -c ../bio/core/bgzf/compress.d
> > [132/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_call.d.o' -c ../bio/core/call.d
> > [133/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_fastq.d.o' -c ../bio/core/fastq.d
> > [134/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_fasta.d.o' -c ../bio/core/fasta.d
> > [135/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_genotype.d.o' -c ../bio/core/genotype.d
> > [136/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_region.d.o' -c ../bio/core/region.d
> > [137/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_kmer.d.o' -c ../bio/core/kmer.d
> > [138/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_sequence.d.o' -c ../bio/core/sequence.d
> > [139/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_algo.d.o' -c ../bio/core/utils/algo.d
> > [140/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_tinymap.d.o' -c ../bio/core/tinymap.d
> > [141/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_exception.d.o' -c ../bio/core/utils/exception.d
> > [142/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_bylinefast.d.o' -c ../bio/core/utils/bylinefast.d
> > [143/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_format.d.o' -c ../bio/core/utils/format.d
> > [144/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_memoize.d.o' -c ../bio/core/utils/memoize.d
> > [145/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_outbuffer.d.o' -c ../bio/core/utils/outbuffer.d
> > [146/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_roundbuf.d.o' -c ../bio/core/utils/roundbuf.d
> > [147/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_stream.d.o' -c ../bio/core/utils/stream.d
> > [148/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_switchendianness.d.o' -c ../bio/core/utils/switchendianness.d
> > [149/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_range.d.o' -c ../bio/core/utils/range.d
> > [150/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_zlib.d.o' -c ../bio/core/utils/zlib.d
> > [151/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_maf_block.d.o' -c ../bio/maf/block.d
> > [152/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_core_utils_tmpfile.d.o' -c ../bio/core/utils/tmpfile.d
> > [153/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_maf_parser.d.o' -c ../bio/maf/parser.d
> > [154/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_maf_reader.d.o' -c ../bio/maf/reader.d
> > [155/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sam_reader.d.o' -c ../bio/sam/reader.d
> > [156/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sam_header.d.o' -c ../bio/sam/header.d
> > [157/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sam_utils_recordparser.d.o' -c ../bio/sam/utils/recordparser.d
> > sam_alignment.rl(51): Warning: statement is not reachable
> > sam_alignment.rl(52): Warning: statement is not reachable
> > sam_alignment.rl(59): Warning: statement is not reachable
> > sam_alignment.rl(60): Warning: statement is not reachable
> > sam_alignment.rl(68): Warning: statement is not reachable
> > sam_alignment.rl(69): Warning: statement is not reachable
> > sam_alignment.rl(76): Warning: statement is not reachable
> > sam_alignment.rl(77): Warning: statement is not reachable
> > sam_alignment.rl(82): Warning: statement is not reachable
> > sam_alignment.rl(83): Warning: statement is not reachable
> > sam_alignment.rl(131): Warning: statement is not reachable
> > sam_alignment.rl(132): Warning: statement is not reachable
> > sam_alignment.rl(163): Warning: statement is not reachable
> > sam_alignment.rl(164): Warning: statement is not reachable
> > sam_alignment.rl(176): Warning: statement is not reachable
> > sam_alignment.rl(177): Warning: statement is not reachable
> > sam_alignment.rl(188): Warning: statement is not reachable
> > sam_alignment.rl(189): Warning: statement is not reachable
> > sam_alignment.rl(221): Warning: statement is not reachable
> > sam_alignment.rl(222): Warning: statement is not reachable
> > sam_alignment.rl(250): Warning: statement is not reachable
> > sam_alignment.rl(252): Warning: statement is not reachable
> > sam_alignment.rl(407): Warning: statement is not reachable
> > sam_alignment.rl(409): Warning: statement is not reachable
> > sam_alignment.rl(51): Warning: statement is not reachable
> > sam_alignment.rl(59): Warning: statement is not reachable
> > sam_alignment.rl(68): Warning: statement is not reachable
> > sam_alignment.rl(76): Warning: statement is not reachable
> > sam_alignment.rl(82): Warning: statement is not reachable
> > sam_alignment.rl(131): Warning: statement is not reachable
> > sam_alignment.rl(163): Warning: statement is not reachable
> > sam_alignment.rl(176): Warning: statement is not reachable
> > sam_alignment.rl(188): Warning: statement is not reachable
> > sam_alignment.rl(221): Warning: statement is not reachable
> > sam_alignment.rl(250): Warning: statement is not reachable
> > sam_alignment.rl(407): Warning: statement is not reachable
> > [158/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sff_constants.d.o' -c ../bio/sff/constants.d
> > [159/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sff_index.d.o' -c ../bio/sff/index.d
> > [160/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sff_read.d.o' -c ../bio/sff/read.d
> > [161/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sam_utils_fastrecordparser.d.o' -c ../bio/sam/utils/fastrecordparser.d
> > sam_alignment.rl(51): Warning: statement is not reachable
> > sam_alignment.rl(59): Warning: statement is not reachable
> > sam_alignment.rl(68): Warning: statement is not reachable
> > sam_alignment.rl(76): Warning: statement is not reachable
> > sam_alignment.rl(82): Warning: statement is not reachable
> > sam_alignment.rl(131): Warning: statement is not reachable
> > sam_alignment.rl(163): Warning: statement is not reachable
> > sam_alignment.rl(176): Warning: statement is not reachable
> > sam_alignment.rl(188): Warning: statement is not reachable
> > sam_alignment.rl(221): Warning: statement is not reachable
> > sam_alignment.rl(250): Warning: statement is not reachable
> > sam_alignment.rl(407): Warning: statement is not reachable
> > sam_alignment.rl(52): Warning: statement is not reachable
> > sam_alignment.rl(60): Warning: statement is not reachable
> > sam_alignment.rl(69): Warning: statement is not reachable
> > sam_alignment.rl(77): Warning: statement is not reachable
> > sam_alignment.rl(83): Warning: statement is not reachable
> > sam_alignment.rl(132): Warning: statement is not reachable
> > sam_alignment.rl(164): Warning: statement is not reachable
> > sam_alignment.rl(177): Warning: statement is not reachable
> > sam_alignment.rl(189): Warning: statement is not reachable
> > sam_alignment.rl(222): Warning: statement is not reachable
> > sam_alignment.rl(252): Warning: statement is not reachable
> > sam_alignment.rl(409): Warning: statement is not reachable
> > sam_alignment.rl(51): Warning: statement is not reachable
> > sam_alignment.rl(59): Warning: statement is not reachable
> > sam_alignment.rl(68): Warning: statement is not reachable
> > sam_alignment.rl(76): Warning: statement is not reachable
> > sam_alignment.rl(82): Warning: statement is not reachable
> > sam_alignment.rl(131): Warning: statement is not reachable
> > sam_alignment.rl(163): Warning: statement is not reachable
> > sam_alignment.rl(176): Warning: statement is not reachable
> > sam_alignment.rl(188): Warning: statement is not reachable
> > sam_alignment.rl(221): Warning: statement is not reachable
> > sam_alignment.rl(250): Warning: statement is not reachable
> > sam_alignment.rl(407): Warning: statement is not reachable
> > [162/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sff_reader.d.o' -c ../bio/sff/reader.d
> > [163/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sff_utils_roundup.d.o' -c ../bio/sff/utils/roundup.d
> > [164/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sff_readrange.d.o' -c ../bio/sff/readrange.d
> > [165/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio_sff_writer.d.o' -c ../bio/sff/writer.d
> > [166/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_bam_header.d.o' -c ../bio2/bam/header.d
> > [167/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_bam_writer.d.o' -c ../bio2/bam/writer.d
> > [168/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_bam_reader.d.o' -c ../bio2/bam/reader.d
> > [169/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_bgzf.d.o' -c ../bio2/bgzf.d
> > [170/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_constants.d.o' -c ../bio2/constants.d
> > [171/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_hashing.d.o' -c ../bio2/hashing.d
> > [172/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_logger.d.o' -c ../bio2/logger.d
> > [173/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_bgzf_writer.d.o' -c ../bio2/bgzf_writer.d
> > [174/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_reads.d.o' -c ../bio2/reads.d
> > [175/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_pileup.d.o' -c ../bio2/pileup.d
> > [176/177] ldc2 -I=biod_test at exe -I=. -I=.. -I/usr/include/d -enable-color -O -g -release -wi -unittest -of='biod_test at exe/bio2_unpack.d.o' -c ../bio2/unpack.d
> > [177/177] ldc2 -of=biod_test 'biod_test at exe/test_unittests.d.o' 'biod_test at exe/bio_bam_abstractreader.d.o' 'biod_test at exe/bio_bam_bai_bin.d.o' 'biod_test at exe/bio_bam_baifile.d.o' 'biod_test at exe/bio_bam_bai_indexing.d.o' 'biod_test at exe/bio_bam_baseinfo.d.o' 'biod_test at exe/bio_bam_cigar.d.o' 'biod_test at exe/bio_bam_constants.d.o' 'biod_test at exe/bio_bam_iontorrent_flowcall.d.o' 'biod_test at exe/bio_bam_iontorrent_flowindex.d.o' 'biod_test at exe/bio_bam_md_core.d.o' 'biod_test at exe/bio_bam_md_operation.d.o' 'biod_test at exe/bio_bam_md_parse.d.o' 'biod_test at exe/bio_bam_md_reconstruct.d.o' 'biod_test at exe/bio_bam_multireader.d.o' 'biod_test at exe/bio_bam_pileup.d.o' 'biod_test at exe/bio_bam_randomaccessmanager.d.o' 'biod_test at exe/bio_bam_read.d.o' 'biod_test at exe/bio_bam_reader.d.o' 'biod_test at exe/bio_bam_readrange.d.o' 'biod_test at exe/bio_bam_reference.d.o' 'biod_test at exe/bio_bam_referenceinfo.d.o' 'biod_test at exe/bio_bam_region.d.o' 'biod_test at exe/bio_bam_snpcallers_maq.d.o' 'biod_test at exe/bio_bam_snpcallers_simple.d.o' 'biod_test at exe/bio_bam_splitter.d.o' 'biod_test at exe/bio_bam_tagvalue.d.o' 'biod_test at exe/bio_bam_thirdparty_msgpack.d.o' 'biod_test at exe/bio_bam_utils_array.d.o' 'biod_test at exe/bio_bam_utils_graph.d.o' 'biod_test at exe/bio_bam_utils_samheadermerger.d.o' 'biod_test at exe/bio_bam_utils_value.d.o' 'biod_test at exe/bio_bam_validation_alignment.d.o' 'biod_test at exe/bio_bam_validation_samheader.d.o' 'biod_test at exe/bio_bam_writer.d.o' 'biod_test at exe/bio_core_base.d.o' 'biod_test at exe/bio_core_bgzf_block.d.o' 'biod_test at exe/bio_core_bgzf_chunk.d.o' 'biod_test at exe/bio_core_bgzf_compress.d.o' 'biod_test at exe/bio_core_bgzf_constants.d.o' 'biod_test at exe/bio_core_bgzf_inputstream.d.o' 'biod_test at exe/bio_core_bgzf_outputstream.d.o' 'biod_test at exe/bio_core_bgzf_virtualoffset.d.o' 'biod_test at exe/bio_core_call.d.o' 'biod_test at exe/bio_core_fasta.d.o' 'biod_test at exe/bio_core_fastq.d.o' 'biod_test at exe/bio_core_genotype.d.o' 'biod_test at exe/bio_core_kmer.d.o' 'biod_test at exe/bio_core_region.d.o' 'biod_test at exe/bio_core_sequence.d.o' 'biod_test at exe/bio_core_tinymap.d.o' 'biod_test at exe/bio_core_utils_algo.d.o' 'biod_test at exe/bio_core_utils_bylinefast.d.o' 'biod_test at exe/bio_core_utils_exception.d.o' 'biod_test at exe/bio_core_utils_format.d.o' 'biod_test at exe/bio_core_utils_memoize.d.o' 'biod_test at exe/bio_core_utils_outbuffer.d.o' 'biod_test at exe/bio_core_utils_range.d.o' 'biod_test at exe/bio_core_utils_roundbuf.d.o' 'biod_test at exe/bio_core_utils_stream.d.o' 'biod_test at exe/bio_core_utils_switchendianness.d.o' 'biod_test at exe/bio_core_utils_tmpfile.d.o' 'biod_test at exe/bio_core_utils_zlib.d.o' 'biod_test at exe/bio_maf_block.d.o' 'biod_test at exe/bio_maf_parser.d.o' 'biod_test at exe/bio_maf_reader.d.o' 'biod_test at exe/bio_sam_header.d.o' 'biod_test at exe/bio_sam_reader.d.o' 'biod_test at exe/bio_sam_utils_fastrecordparser.d.o' 'biod_test at exe/bio_sam_utils_recordparser.d.o' 'biod_test at exe/bio_sff_constants.d.o' 'biod_test at exe/bio_sff_index.d.o' 'biod_test at exe/bio_sff_read.d.o' 'biod_test at exe/bio_sff_reader.d.o' 'biod_test at exe/bio_sff_readrange.d.o' 'biod_test at exe/bio_sff_utils_roundup.d.o' 'biod_test at exe/bio_sff_writer.d.o' 'biod_test at exe/bio2_bam_header.d.o' 'biod_test at exe/bio2_bam_reader.d.o' 'biod_test at exe/bio2_bam_writer.d.o' 'biod_test at exe/bio2_bgzf.d.o' 'biod_test at exe/bio2_bgzf_writer.d.o' 'biod_test at exe/bio2_constants.d.o' 'biod_test at exe/bio2_hashing.d.o' 'biod_test at exe/bio2_logger.d.o' 'biod_test at exe/bio2_pileup.d.o' 'biod_test at exe/bio2_reads.d.o' 'biod_test at exe/bio2_unpack.d.o' -O -g -release -wi -L=-z -L=relro -L=-z -L=now -L=-lundead -L=-lz
> > dh_auto_test
> > cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 MESON_TESTTHREADS=2 ninja test
> > [0/1] Running all tests.
> > 1/1 biod_tests FAIL 0.27 s (killed by signal 11 SIGSEGV)
> >
> > Ok: 0
> > Expected Fail: 0
> > Fail: 1
> > Unexpected Pass: 0
> > Skipped: 0
> > Timeout: 0
> >
> >
> > The output from the failed tests:
> >
> > 1/1 biod_tests FAIL 0.27 s (killed by signal 11 SIGSEGV)
> >
> > --- command ---
> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/biod_test
> > --- stderr ---
> > Running unittests...
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D4core7runtime18runModuleUnitTestsUZ19unittestSegvHandlerUNbiPSQCk3sys5posix6signal9siginfo_tPvZv+0x27)[0x7fbb8489cbf7]
> > /lib/x86_64-linux-gnu/libpthread.so.0(+0x12670)[0x7fbb847e5670]
> > /usr/lib/x86_64-linux-gnu/libphobos2-ldc-shared.so.82(_D3std11parallelism8TaskPool16tryDeleteExecuteMFPSQBwQBv12AbstractTaskZv+0xa)[0x7fbb84bc0c4a]
> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/biod_test(+0x12d07e)[0x55a60eb3607e]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(rt_finalizeFromGC+0xab)[0x7fbb848c33eb]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D2gc4impl12conservativeQw3Gcx5sweepMFNbZm+0x2ef)[0x7fbb848ad7bf]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D2gc4impl12conservativeQw3Gcx11fullcollectMFNbbZm+0x192)[0x7fbb848aa9b2]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D2gc4impl12conservativeQw3Gcx8bigAllocMFNbmKmkxC8TypeInfoZPv+0xda)[0x7fbb848ac3ca]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D2gc4impl12conservativeQw14ConservativeGC__T9runLockedS_DQCeQCeQCcQCnQBs12mallocNoSyncMFNbmkKmxC8TypeInfoZPvS_DQEgQEgQEeQEp10mallocTimelS_DQFiQFiQFgQFr10numMallocslTmTkTmTxQCzZQFcMFNbKmKkKmKxQDsZQDl+0x94)[0x7fbb848a8c74]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_DThn16_2gc4impl12conservativeQw14ConservativeGC6qallocMFNbmkxC8TypeInfoZS4core6memory8BlkInfo_+0x4f)[0x7fbb848ab2df]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(gc_qalloc+0x20)[0x7fbb848afbd0]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D4core6memory2GC6qallocFNaNbmkxC8TypeInfoZSQBqQBo8BlkInfo_+0x12)[0x7fbb8489bfb2]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_d_newarrayU+0x169)[0x7fbb848c2519]
> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/biod_test(+0x135dd6)[0x55a60eb3edd6]
> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/biod_test(+0x14d474)[0x55a60eb56474]
> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/biod_test(+0x7b043)[0x55a60ea84043]
> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/biod_test(+0xda11c)[0x55a60eae311c]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D4core7runtime18runModuleUnitTestsUZ14__foreachbody2MFPS6object10ModuleInfoZi+0x1c)[0x7fbb8489cc2c]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D2rt5minfo17moduleinfos_applyFMDFyPS6object10ModuleInfoZiZ14__foreachbody2MFKSQCz19sections_elf_shared3DSOZi+0x32)[0x7fbb848c89f2]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D2rt19sections_elf_shared3DSO7opApplyFMDFKSQBqQBqQyZiZi+0x4a)[0x7fbb848ca00a]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D2rt5minfo17moduleinfos_applyFMDFyPS6object10ModuleInfoZiZi+0x1c)[0x7fbb848c899c]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D6object10ModuleInfo7opApplyFMDFPSQBhQBdZiZi+0x1f)[0x7fbb848b2e6f]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(runModuleUnitTests+0x129)[0x7fbb8489ca49]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_D2rt6dmain211_d_run_mainUiPPaPUAAaZiZ6runAllMFZv+0x1b)[0x7fbb848bf0fb]
> > /usr/lib/x86_64-linux-gnu/libdruntime-ldc-shared.so.82(_d_run_main+0x1f6)[0x7fbb848bef46]
> > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb)[0x7fbb8449909b]
> > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/biod_test(+0x7864a)[0x55a60ea8164a]
> > -------
> >
> > Full log written to /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/meson-logs/testlog.txt
> > FAILED: meson-test
> > /usr/bin/meson test --no-rebuild --print-errorlogs
> > ninja: build stopped: subcommand failed.
> > dh_auto_test: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 MESON_TESTTHREADS=2 ninja test returned exit code 1
>
> The full build log is available from:
> http://aws-logs.debian.net/2018/12/29/libbiod_0.2.1-1_unstable.log
>
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
>
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
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