Your message dated Fri, 04 Aug 2017 17:19:56 +0000
with message-id <e1ddggs-0000bc...@fasolo.debian.org>
and subject line Bug#868455: fixed in libbiod 0.1.0-4
has caused the Debian Bug report #868455,
regarding libbiod: FTBFS with new ldc?
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
868455: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=868455
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: libbiod
Severity: serious
Version: 0.1.0-3
Hello, seems the latest changes in unstable somewhat broke libbiod linker.
ldc2 -of biod_test 'biod_test@exe/test_unittests.d.o'
'biod_test@exe/bio_bam_utils_value.d.o'
'biod_test@exe/bio_bam_utils_samheadermerger.d.o'
'biod_test@exe/bio_bam_utils_array.d.o' 'biod_test@exe/bio_bam_utils_graph.d.o'
'biod_test@exe/bio_bam_pileup.d.o' 'biod_test@exe/bio_bam_readrange.d.o'
'biod_test@exe/bio_bam_reader.d.o'
'biod_test@exe/bio_bam_thirdparty_msgpack.d.o'
'biod_test@exe/bio_bam_baifile.d.o'
'biod_test@exe/bio_bam_iontorrent_flowcall.d.o'
'biod_test@exe/bio_bam_iontorrent_flowindex.d.o'
'biod_test@exe/bio_bam_splitter.d.o' 'biod_test@exe/bio_bam_abstractreader.d.o'
'biod_test@exe/bio_bam_bai_indexing.d.o' 'biod_test@exe/bio_bam_bai_bin.d.o'
'biod_test@exe/bio_bam_multireader.d.o' 'biod_test@exe/bio_bam_reference.d.o'
'biod_test@exe/bio_bam_md_operation.d.o' 'biod_test@exe/bio_bam_md_core.d.o'
'biod_test@exe/bio_bam_md_parse.d.o' 'biod_test@exe/bio_bam_md_reconstruct.d.o'
'biod_test@exe/bio_bam_tagvalue.d.o'
'biod_test@exe/bio_bam_validation_alignment.d.o'
'biod_test@exe/bio_bam_validation_samheader.d.o'
'biod_test@exe/bio_bam_region.d.o'
'biod_test@exe/bio_bam_randomaccessmanager.d.o'
'biod_test@exe/bio_bam_referenceinfo.d.o' 'biod_test@exe/bio_bam_constants.d.o'
'biod_test@exe/bio_bam_snpcallers_maq.d.o'
'biod_test@exe/bio_bam_snpcallers_simple.d.o' 'biod_test@exe/bio_bam_read.d.o'
'biod_test@exe/bio_bam_writer.d.o' 'biod_test@exe/bio_bam_baseinfo.d.o'
'biod_test@exe/bio_maf_reader.d.o' 'biod_test@exe/bio_maf_parser.d.o'
'biod_test@exe/bio_maf_block.d.o' 'biod_test@exe/bio_core_utils_memoize.d.o'
'biod_test@exe/bio_core_utils_algo.d.o'
'biod_test@exe/bio_core_utils_stream.d.o'
'biod_test@exe/bio_core_utils_zlib.d.o'
'biod_test@exe/bio_core_utils_tmpfile.d.o'
'biod_test@exe/bio_core_utils_roundbuf.d.o'
'biod_test@exe/bio_core_utils_format.d.o'
'biod_test@exe/bio_core_utils_bylinefast.d.o'
'biod_test@exe/bio_core_utils_range.d.o'
'biod_test@exe/bio_core_utils_switchendianness.d.o'
'biod_test@exe/bio_core_utils_outbuffer.d.o'
'biod_test@exe/bio_core_genotype.d.o' 'biod_test@exe/bio_core_fasta.d.o'
'biod_test@exe/bio_core_base.d.o' 'biod_test@exe/bio_core_kmer.d.o'
'biod_test@exe/bio_core_region.d.o' 'biod_test@exe/bio_core_tinymap.d.o'
'biod_test@exe/bio_core_sequence.d.o'
'biod_test@exe/bio_core_bgzf_outputstream.d.o'
'biod_test@exe/bio_core_bgzf_chunk.d.o'
'biod_test@exe/bio_core_bgzf_inputstream.d.o'
'biod_test@exe/bio_core_bgzf_constants.d.o'
'biod_test@exe/bio_core_bgzf_block.d.o'
'biod_test@exe/bio_core_bgzf_virtualoffset.d.o'
'biod_test@exe/bio_core_bgzf_compress.d.o' 'biod_test@exe/bio_core_call.d.o'
'biod_test@exe/bio_sff_utils_roundup.d.o' 'biod_test@exe/bio_sff_index.d.o'
'biod_test@exe/bio_sff_readrange.d.o' 'biod_test@exe/bio_sff_reader.d.o'
'biod_test@exe/bio_sff_constants.d.o' 'biod_test@exe/bio_sff_read.d.o'
'biod_test@exe/bio_sff_writer.d.o'
'biod_test@exe/bio_sam_utils_fastrecordparser.d.o'
'biod_test@exe/bio_sam_utils_recordparser.d.o'
'biod_test@exe/bio_sam_reader.d.o' 'biod_test@exe/bio_sam_header.d.o' -O -g
-release -L-z -Lrelro -L-z -Lnow -L-lundead -L-lz
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi':
(.text._D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi[_D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi]+0x11f2):
undefined reference to `_D3std3utf7toUTF16FNaNfxAaZAyu'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi':
(.text._D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi[_D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi]+0x1213):
undefined reference to `_D3std3utf7toUTF32FNaNfxAaZAyw'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv':
(.text._D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv[_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv]+0x540):
undefined reference to `_D3std3utf6toUTF8FNaNfxAuZAya'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv':
(.text._D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv[_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv]+0x5bf):
undefined reference to `_D3std3utf6toUTF8FNaNfxAwZAya'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv':
(.text._D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv[_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv]+0x11a3):
undefined reference to `_D3std3utf6toUTF8FNaNfxAwZAya'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv':
(.text._D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv[_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv]+0x128a):
undefined reference to `_D3std3utf6toUTF8FNaNfxAuZAya'
collect2: error: ld returned 1 exit status
Buildlog attached
G.
[0;34mD: cmdline: build --distribution sid --buildresult
/home/locutus/pbuilder/sid_result --basetgz /home/locutus/pbuilder/sid-base.tgz
--logfile /home/locutus/pbuilder/sid_result/libbiod_0.1.0-3_amd64.build
--mirror http://httpredir.debian.org/debian --debootstrapopts
--keyring=/usr/share/keyrings/debian-archive-keyring.gpg --aptcache
/home/locutus/pbuilder/aptcache/debian --components main contrib non-free
libbiod_0.1.0-3.dsc[0m
[0mI: using fakeroot in build.[0m
[0mI: pbuilder: network access will be disabled during build[0m
[0mI: Current time: Sat Jul 15 16:36:52 CEST 2017[0m
[0mI: pbuilder-time-stamp: 1500129412[0m
[0mI: Building the build Environment[0m
[0mI: extracting base tarball [/home/locutus/pbuilder/sid-base.tgz][0m
[0mI: copying local configuration[0m
[1;33mW: --override-config is not set; not updating apt.conf Read the manpage
for details.[0m
[0mI: mounting /proc filesystem[0m
[0mI: mounting /sys filesystem[0m
[0mI: creating /{dev,run}/shm[0m
[0mI: mounting /dev/pts filesystem[0m
[0mI: policy-rc.d already exists[0m
[0mI: Obtaining the cached apt archive contents[0m
[0mI: Copying source file[0m
[0mI: copying [libbiod_0.1.0-3.dsc][0m
[0mI: copying [./libbiod_0.1.0.orig.tar.gz][0m
[0mI: copying [./libbiod_0.1.0-3.debian.tar.xz][0m
[0mI: Extracting source[0m
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/home/locutus/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Apr 10 08:09:46 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "ti...@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libbiod_0.1.0-3.dsc
dpkg-source: info: extracting libbiod in libbiod-0.1.0
dpkg-source: info: unpacking libbiod_0.1.0.orig.tar.gz
dpkg-source: info: unpacking libbiod_0.1.0-3.debian.tar.xz
dpkg-source: info: applying 0002-improved-big-endian-support.patch
dpkg-source: info: applying 0003-include-the-AH-header-tag-to-SQ-lines.patch
dpkg-source: info: applying 0004-use-consistent-naming-21.patch
dpkg-source: info: applying 0005-fixes-lomereiter-sambamba-244.patch
dpkg-source: info: applying 0006-switch-to-undead.stream.patch
dpkg-source: info: applying 0007-std.c-core.stdc.patch
dpkg-source: info: applying 0008-fix-deprecations-and-some-warnings.patch
dpkg-source: info: applying 0009-fix-toHash-signature.patch
dpkg-source: info: applying
0011-better-.travis.yml-uses-dub-test-and-tests-ldc.patch
dpkg-source: info: applying
0013-fix-toJSON-usage-for-new-and-old-compilers.patch
dpkg-source: info: applying
0014-Add-compareCoordinatesAndStrand-to-fix-sorting-test-.patch
dpkg-source: info: applying 0015-Add-Meson-build-definition.patch
dpkg-source: info: applying 0016-fix-type-conversion.patch
[0mI: Installing the build-deps[0m
-> Attempting to parse the build-deps
-> Considering build-depdebhelper (>= 10)
-> Trying to add debhelper
-> Considering build-dep ldc
-> Trying to add ldc
-> Considering build-dep meson (>= 0.38)
-> Trying to add meson
-> Considering build-dep pkg-config
-> Trying to add pkg-config
-> Considering build-dep libundead-dev
-> Trying to add libundead-dev
-> Considering build-dep zlib1g-dev
-> Trying to add zlib1g-dev
-> Installing debhelper ldc meson pkg-config libundead-dev zlib1g-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils dh-autoreconf
dh-python dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libconfig9 libcroco3 libedit2
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libllvm3.9
libmagic-mgc libmagic1 libmpdec2 libncurses5 libphobos2-ldc-dev
libphobos2-ldc72 libpipeline1 libpython3-stdlib libpython3.5-minimal
libpython3.5-stdlib libreadline7 libsigsegv2 libsqlite3-0 libssl1.1
libtimedate-perl libtool libxml2 m4 man-db mime-support ninja-build
po-debconf python3 python3-minimal python3.5 python3.5-minimal
readline-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.5-venv
python3.5-doc binfmt-support readline-doc
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism file gettext gettext-base
groff-base intltool-debian ldc libarchive-zip-perl libbsd0 libconfig9
libcroco3 libedit2 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0
libicu57 libllvm3.9 libmagic-mgc libmagic1 libmpdec2 libncurses5
libphobos2-ldc-dev libphobos2-ldc72 libpipeline1 libpython3-stdlib
libpython3.5-minimal libpython3.5-stdlib libreadline7 libsigsegv2
libsqlite3-0 libssl1.1 libtimedate-perl libtool libundead-dev libxml2 m4
man-db meson mime-support ninja-build pkg-config po-debconf python3
python3-minimal python3.5 python3.5-minimal readline-common zlib1g-dev
0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.1 MB/48.0 MB of archives.
After this operation, 238 MB of additional disk space will be used.
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2.2.2-1 [86.4 kB]
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1:1.2.0-1 [1295 kB]
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amd64 1.0.6-2 [158 kB]
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1.7.2-3 [93.1 kB]
Get:11 http://cdn-fastly.deb.debian.org/debian sid/main amd64 meson all
0.41.1-1 [179 kB]
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libfakeroot
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fakeroot libfakeroot
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[0mI: Copying back the cached apt archive contents[0m
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[0mI: Building the package[0m
[0mI: Running cd /build/libbiod-0.1.0/ && env
PATH="/usr/sbin:/usr/bin:/sbin:/bin" HOME="/nonexistent" dpkg-buildpackage -us
-uc -rfakeroot[0m
dpkg-buildpackage: info: source package libbiod
dpkg-buildpackage: info: source version 0.1.0-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <ti...@debian.org>
dpkg-source --before-build libbiod-0.1.0
dpkg-buildpackage: info: host architecture amd64
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
dh_autoreconf_clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/libbiod-0.1.0'
rm -rf build/
dh_clean
make[1]: Leaving directory '/build/libbiod-0.1.0'
dpkg-source -b libbiod-0.1.0
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building libbiod using existing ./libbiod_0.1.0.orig.tar.gz
dpkg-source: info: building libbiod in libbiod_0.1.0-3.debian.tar.xz
dpkg-source: info: building libbiod in libbiod_0.1.0-3.dsc
debian/rules build
dh build
dh_testdir
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/libbiod-0.1.0'
mkdir build
(cd build && meson --prefix=/usr --buildtype=plain ..)
WARNING: You are using 'ANSI_X3.4-1968' which is not a a Unicode-compatible
locale.
WARNING: You might see errors if you use UTF-8 strings as filenames, as
strings, or as file contents.
WARNING: Please switch to a UTF-8 locale for your platform.
The Meson build system
Version: 0.41.1
Source dir: /build/libbiod-0.1.0
Build dir: /build/libbiod-0.1.0/build
Build type: native build
Project name: BioD
Native d compiler: ldc2 (llvm 1.2.0)
Appending DFLAGS from environment: '-O -g -release'
Appending LDFLAGS from environment: '-Wl,-z,relro -Wl,-z,now'
Build machine cpu family: x86_64
Build machine cpu: x86_64
Found pkg-config: /usr/bin/pkg-config (0.29)
Native dependency undead found: YES 1.0.6
Native dependency zlib found: YES 1.2.8
Build targets in project: 2
make[1]: Leaving directory '/build/libbiod-0.1.0'
debian/rules override_dh_auto_build
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ninja -Cbuild -v
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[1/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[24/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[25/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[26/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[27/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[28/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[29/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[30/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[31/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[34/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[35/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[36/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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[37/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_utils_format.d.o' -c
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-g -release -relocation-model=pic -of
'biod@sha/bio_core_utils_switchendianness.d.o' -c
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_utils_range.d.o' -c
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_utils_bylinefast.d.o'
-c ../bio/core/utils/bylinefast.d
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-g -release -relocation-model=pic -of
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_utils_outbuffer.d.o'
-c ../bio/core/utils/outbuffer.d
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_kmer.d.o' -c
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_bgzf_compress.d.o' -c
../bio/core/bgzf/compress.d
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-g -release -relocation-model=pic -of
'biod@sha/bio_core_bgzf_virtualoffset.d.o' -c ../bio/core/bgzf/virtualoffset.d
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-g -release -relocation-model=pic -of 'biod@sha/bio_sff_utils_roundup.d.o' -c
../bio/sff/utils/roundup.d
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-g -release -relocation-model=pic -of 'biod@sha/bio_sff_index.d.o' -c
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_bgzf_block.d.o' -c
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-g -release -relocation-model=pic -of 'biod@sha/bio_bam_read.d.o' -c
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-g -release -relocation-model=pic -of 'biod@sha/bio_sff_reader.d.o' -c
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-g -release -relocation-model=pic -of 'biod@sha/bio_sff_writer.d.o' -c
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_bgzf_inputstream.d.o'
-c ../bio/core/bgzf/inputstream.d
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-g -release -relocation-model=pic -of
'biod@sha/bio_core_bgzf_outputstream.d.o' -c ../bio/core/bgzf/outputstream.d
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-g -release -relocation-model=pic -of
'biod@sha/bio_sam_utils_recordparser.d.o' -c ../bio/sam/utils/recordparser.d
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-g -release -relocation-model=pic -of 'biod@sha/bio_core_fasta.d.o' -c
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_tagvalue.d.o' -c ../bio/bam/tagvalue.d
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-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_bam_md_core.d.o'
-c ../bio/bam/md/core.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_md_parse.d.o' -c ../bio/bam/md/parse.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_utils_array.d.o' -c ../bio/bam/utils/array.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_validation_alignment.d.o' -c
../bio/bam/validation/alignment.d
[77/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_utils_value.d.o' -c ../bio/bam/utils/value.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_utils_graph.d.o' -c ../bio/bam/utils/graph.d
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-g -release -relocation-model=pic -of
'biod@sha/bio_sam_utils_fastrecordparser.d.o' -c
../bio/sam/utils/fastrecordparser.d
[80/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_tinymap.d.o' -c ../bio/core/tinymap.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_md_operation.d.o' -c ../bio/bam/md/operation.d
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-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_bam_baifile.d.o'
-c ../bio/bam/baifile.d
[83/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_readrange.d.o' -c ../bio/bam/readrange.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_iontorrent_flowindex.d.o' -c
../bio/bam/iontorrent/flowindex.d
[85/149] ldc2 -Ibiod@sha -I. -I.. -I -I../ -I/usr/include/d/ -enable-color -O
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_splitter.d.o' -c ../bio/bam/splitter.d
[87/149] ldc2 -of libbiod.so.0.1.0 'biod@sha/bio_bam_utils_value.d.o'
'biod@sha/bio_bam_utils_samheadermerger.d.o' 'biod@sha/bio_bam_utils_array.d.o'
'biod@sha/bio_bam_utils_graph.d.o' 'biod@sha/bio_bam_pileup.d.o'
'biod@sha/bio_bam_readrange.d.o' 'biod@sha/bio_bam_reader.d.o'
'biod@sha/bio_bam_thirdparty_msgpack.d.o' 'biod@sha/bio_bam_baifile.d.o'
'biod@sha/bio_bam_iontorrent_flowcall.d.o'
'biod@sha/bio_bam_iontorrent_flowindex.d.o' 'biod@sha/bio_bam_splitter.d.o'
'biod@sha/bio_bam_abstractreader.d.o' 'biod@sha/bio_bam_bai_indexing.d.o'
'biod@sha/bio_bam_bai_bin.d.o' 'biod@sha/bio_bam_multireader.d.o'
'biod@sha/bio_bam_reference.d.o' 'biod@sha/bio_bam_md_operation.d.o'
'biod@sha/bio_bam_md_core.d.o' 'biod@sha/bio_bam_md_parse.d.o'
'biod@sha/bio_bam_md_reconstruct.d.o' 'biod@sha/bio_bam_tagvalue.d.o'
'biod@sha/bio_bam_validation_alignment.d.o'
'biod@sha/bio_bam_validation_samheader.d.o' 'biod@sha/bio_bam_region.d.o'
'biod@sha/bio_bam_randomaccessmanager.d.o' 'biod@sha/bio_bam_referenceinfo.d.o'
'biod@sha/bio_bam_constants.d.o' 'biod@sha/bio_bam_snpcallers_maq.d.o'
'biod@sha/bio_bam_snpcallers_simple.d.o' 'biod@sha/bio_bam_read.d.o'
'biod@sha/bio_bam_writer.d.o' 'biod@sha/bio_bam_baseinfo.d.o'
'biod@sha/bio_maf_reader.d.o' 'biod@sha/bio_maf_parser.d.o'
'biod@sha/bio_maf_block.d.o' 'biod@sha/bio_core_utils_memoize.d.o'
'biod@sha/bio_core_utils_algo.d.o' 'biod@sha/bio_core_utils_stream.d.o'
'biod@sha/bio_core_utils_zlib.d.o' 'biod@sha/bio_core_utils_tmpfile.d.o'
'biod@sha/bio_core_utils_roundbuf.d.o' 'biod@sha/bio_core_utils_format.d.o'
'biod@sha/bio_core_utils_bylinefast.d.o' 'biod@sha/bio_core_utils_range.d.o'
'biod@sha/bio_core_utils_switchendianness.d.o'
'biod@sha/bio_core_utils_outbuffer.d.o' 'biod@sha/bio_core_genotype.d.o'
'biod@sha/bio_core_fasta.d.o' 'biod@sha/bio_core_base.d.o'
'biod@sha/bio_core_kmer.d.o' 'biod@sha/bio_core_region.d.o'
'biod@sha/bio_core_tinymap.d.o' 'biod@sha/bio_core_sequence.d.o'
'biod@sha/bio_core_bgzf_outputstream.d.o' 'biod@sha/bio_core_bgzf_chunk.d.o'
'biod@sha/bio_core_bgzf_inputstream.d.o' 'biod@sha/bio_core_bgzf_constants.d.o'
'biod@sha/bio_core_bgzf_block.d.o' 'biod@sha/bio_core_bgzf_virtualoffset.d.o'
'biod@sha/bio_core_bgzf_compress.d.o' 'biod@sha/bio_core_call.d.o'
'biod@sha/bio_sff_utils_roundup.d.o' 'biod@sha/bio_sff_index.d.o'
'biod@sha/bio_sff_readrange.d.o' 'biod@sha/bio_sff_reader.d.o'
'biod@sha/bio_sff_constants.d.o' 'biod@sha/bio_sff_read.d.o'
'biod@sha/bio_sff_writer.d.o' 'biod@sha/bio_sam_utils_fastrecordparser.d.o'
'biod@sha/bio_sam_utils_recordparser.d.o' 'biod@sha/bio_sam_reader.d.o'
'biod@sha/bio_sam_header.d.o' -L-rpath=/build/libbiod-0.1.0/build/ -shared
-relocation-model=pic -L-soname -Llibbiod.so.0 -O -g -release -L-z -Lrelro -L-z
-Lnow -L-lundead -L-lz
[88/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_md_reconstruct.d.o' -c ../bio/bam/md/reconstruct.d
[89/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_bam_bai_bin.d.o'
-c ../bio/bam/bai/bin.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_abstractreader.d.o' -c ../bio/bam/abstractreader.d
[91/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_iontorrent_flowcall.d.o' -c
../bio/bam/iontorrent/flowcall.d
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-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_bam_reader.d.o'
-c ../bio/bam/reader.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_reference.d.o' -c ../bio/bam/reference.d
[94/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_validation_samheader.d.o' -c
../bio/bam/validation/samheader.d
[95/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_bam_region.d.o'
-c ../bio/bam/region.d
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-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_constants.d.o' -c ../bio/bam/constants.d
[97/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_utils_samheadermerger.d.o' -c
../bio/bam/utils/samheadermerger.d
[98/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_bai_indexing.d.o' -c ../bio/bam/bai/indexing.d
[99/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_referenceinfo.d.o' -c ../bio/bam/referenceinfo.d
[100/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_snpcallers_simple.d.o' -c ../bio/bam/snpcallers/simple.d
[101/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_snpcallers_maq.d.o' -c ../bio/bam/snpcallers/maq.d
[102/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_bam_pileup.d.o'
-c ../bio/bam/pileup.d
[103/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_maf_block.d.o'
-c ../bio/maf/block.d
[104/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_baseinfo.d.o' -c ../bio/bam/baseinfo.d
[105/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_algo.d.o' -c ../bio/core/utils/algo.d
[106/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_maf_reader.d.o'
-c ../bio/maf/reader.d
[107/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_zlib.d.o' -c ../bio/core/utils/zlib.d
[108/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_bam_writer.d.o'
-c ../bio/bam/writer.d
[109/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_roundbuf.d.o' -c ../bio/core/utils/roundbuf.d
[110/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_format.d.o' -c ../bio/core/utils/format.d
[111/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_stream.d.o' -c ../bio/core/utils/stream.d
[112/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_thirdparty_msgpack.d.o' -c
../bio/bam/thirdparty/msgpack.d
[113/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_switchendianness.d.o' -c
../bio/core/utils/switchendianness.d
[114/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_tmpfile.d.o' -c ../bio/core/utils/tmpfile.d
[115/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_outbuffer.d.o' -c ../bio/core/utils/outbuffer.d
[116/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_bylinefast.d.o' -c ../bio/core/utils/bylinefast.d
[117/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_genotype.d.o' -c ../bio/core/genotype.d
[118/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_maf_parser.d.o'
-c ../bio/maf/parser.d
[119/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_core_base.d.o'
-c ../bio/core/base.d
[120/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_core_region.d.o'
-c ../bio/core/region.d
[121/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_core_kmer.d.o'
-c ../bio/core/kmer.d
[122/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_bgzf_chunk.d.o' -c ../bio/core/bgzf/chunk.d
[123/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_memoize.d.o' -c ../bio/core/utils/memoize.d
[124/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_bgzf_constants.d.o' -c ../bio/core/bgzf/constants.d
[125/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_utils_range.d.o' -c ../bio/core/utils/range.d
[126/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_sequence.d.o' -c ../bio/core/sequence.d
[127/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_bgzf_block.d.o' -c ../bio/core/bgzf/block.d
[128/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_bgzf_virtualoffset.d.o' -c
../bio/core/bgzf/virtualoffset.d
[129/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_sff_utils_roundup.d.o' -c ../bio/sff/utils/roundup.d
[130/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_bgzf_compress.d.o' -c ../bio/core/bgzf/compress.d
[131/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_sff_index.d.o'
-c ../bio/sff/index.d
[132/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_core_call.d.o'
-c ../bio/core/call.d
[133/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_sff_constants.d.o' -c ../bio/sff/constants.d
[134/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_sff_read.d.o' -c
../bio/sff/read.d
[135/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_bgzf_inputstream.d.o' -c ../bio/core/bgzf/inputstream.d
[136/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_sff_reader.d.o'
-c ../bio/sff/reader.d
[137/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_sff_readrange.d.o' -c ../bio/sff/readrange.d
[138/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_sff_writer.d.o'
-c ../bio/sff/writer.d
[139/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_randomaccessmanager.d.o' -c
../bio/bam/randomaccessmanager.d
[140/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_core_fasta.d.o'
-c ../bio/core/fasta.d
[141/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_core_bgzf_outputstream.d.o' -c
../bio/core/bgzf/outputstream.d
[142/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_bam_read.d.o' -c
../bio/bam/read.d
[143/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_bam_multireader.d.o' -c ../bio/bam/multireader.d
[144/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_sam_reader.d.o'
-c ../bio/sam/reader.d
[145/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_sam_utils_recordparser.d.o' -c
../bio/sam/utils/recordparser.d
[146/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/bio_sam_header.d.o'
-c ../bio/sam/header.d
[147/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of
'biod_test@exe/bio_sam_utils_fastrecordparser.d.o' -c
../bio/sam/utils/fastrecordparser.d
[148/149] ldc2 -Ibiod_test@exe -I. -I.. -I -I../ -I/usr/include/d/
-enable-color -O -g -release -unittest -of 'biod_test@exe/test_unittests.d.o'
-c ../test/unittests.d
[149/149] ldc2 -of biod_test 'biod_test@exe/test_unittests.d.o'
'biod_test@exe/bio_bam_utils_value.d.o'
'biod_test@exe/bio_bam_utils_samheadermerger.d.o'
'biod_test@exe/bio_bam_utils_array.d.o' 'biod_test@exe/bio_bam_utils_graph.d.o'
'biod_test@exe/bio_bam_pileup.d.o' 'biod_test@exe/bio_bam_readrange.d.o'
'biod_test@exe/bio_bam_reader.d.o'
'biod_test@exe/bio_bam_thirdparty_msgpack.d.o'
'biod_test@exe/bio_bam_baifile.d.o'
'biod_test@exe/bio_bam_iontorrent_flowcall.d.o'
'biod_test@exe/bio_bam_iontorrent_flowindex.d.o'
'biod_test@exe/bio_bam_splitter.d.o' 'biod_test@exe/bio_bam_abstractreader.d.o'
'biod_test@exe/bio_bam_bai_indexing.d.o' 'biod_test@exe/bio_bam_bai_bin.d.o'
'biod_test@exe/bio_bam_multireader.d.o' 'biod_test@exe/bio_bam_reference.d.o'
'biod_test@exe/bio_bam_md_operation.d.o' 'biod_test@exe/bio_bam_md_core.d.o'
'biod_test@exe/bio_bam_md_parse.d.o' 'biod_test@exe/bio_bam_md_reconstruct.d.o'
'biod_test@exe/bio_bam_tagvalue.d.o'
'biod_test@exe/bio_bam_validation_alignment.d.o'
'biod_test@exe/bio_bam_validation_samheader.d.o'
'biod_test@exe/bio_bam_region.d.o'
'biod_test@exe/bio_bam_randomaccessmanager.d.o'
'biod_test@exe/bio_bam_referenceinfo.d.o' 'biod_test@exe/bio_bam_constants.d.o'
'biod_test@exe/bio_bam_snpcallers_maq.d.o'
'biod_test@exe/bio_bam_snpcallers_simple.d.o' 'biod_test@exe/bio_bam_read.d.o'
'biod_test@exe/bio_bam_writer.d.o' 'biod_test@exe/bio_bam_baseinfo.d.o'
'biod_test@exe/bio_maf_reader.d.o' 'biod_test@exe/bio_maf_parser.d.o'
'biod_test@exe/bio_maf_block.d.o' 'biod_test@exe/bio_core_utils_memoize.d.o'
'biod_test@exe/bio_core_utils_algo.d.o'
'biod_test@exe/bio_core_utils_stream.d.o'
'biod_test@exe/bio_core_utils_zlib.d.o'
'biod_test@exe/bio_core_utils_tmpfile.d.o'
'biod_test@exe/bio_core_utils_roundbuf.d.o'
'biod_test@exe/bio_core_utils_format.d.o'
'biod_test@exe/bio_core_utils_bylinefast.d.o'
'biod_test@exe/bio_core_utils_range.d.o'
'biod_test@exe/bio_core_utils_switchendianness.d.o'
'biod_test@exe/bio_core_utils_outbuffer.d.o'
'biod_test@exe/bio_core_genotype.d.o' 'biod_test@exe/bio_core_fasta.d.o'
'biod_test@exe/bio_core_base.d.o' 'biod_test@exe/bio_core_kmer.d.o'
'biod_test@exe/bio_core_region.d.o' 'biod_test@exe/bio_core_tinymap.d.o'
'biod_test@exe/bio_core_sequence.d.o'
'biod_test@exe/bio_core_bgzf_outputstream.d.o'
'biod_test@exe/bio_core_bgzf_chunk.d.o'
'biod_test@exe/bio_core_bgzf_inputstream.d.o'
'biod_test@exe/bio_core_bgzf_constants.d.o'
'biod_test@exe/bio_core_bgzf_block.d.o'
'biod_test@exe/bio_core_bgzf_virtualoffset.d.o'
'biod_test@exe/bio_core_bgzf_compress.d.o' 'biod_test@exe/bio_core_call.d.o'
'biod_test@exe/bio_sff_utils_roundup.d.o' 'biod_test@exe/bio_sff_index.d.o'
'biod_test@exe/bio_sff_readrange.d.o' 'biod_test@exe/bio_sff_reader.d.o'
'biod_test@exe/bio_sff_constants.d.o' 'biod_test@exe/bio_sff_read.d.o'
'biod_test@exe/bio_sff_writer.d.o'
'biod_test@exe/bio_sam_utils_fastrecordparser.d.o'
'biod_test@exe/bio_sam_utils_recordparser.d.o'
'biod_test@exe/bio_sam_reader.d.o' 'biod_test@exe/bio_sam_header.d.o' -O -g
-release -L-z -Lrelro -L-z -Lnow -L-lundead -L-lz
FAILED: biod_test
ldc2 -of biod_test 'biod_test@exe/test_unittests.d.o'
'biod_test@exe/bio_bam_utils_value.d.o'
'biod_test@exe/bio_bam_utils_samheadermerger.d.o'
'biod_test@exe/bio_bam_utils_array.d.o' 'biod_test@exe/bio_bam_utils_graph.d.o'
'biod_test@exe/bio_bam_pileup.d.o' 'biod_test@exe/bio_bam_readrange.d.o'
'biod_test@exe/bio_bam_reader.d.o'
'biod_test@exe/bio_bam_thirdparty_msgpack.d.o'
'biod_test@exe/bio_bam_baifile.d.o'
'biod_test@exe/bio_bam_iontorrent_flowcall.d.o'
'biod_test@exe/bio_bam_iontorrent_flowindex.d.o'
'biod_test@exe/bio_bam_splitter.d.o' 'biod_test@exe/bio_bam_abstractreader.d.o'
'biod_test@exe/bio_bam_bai_indexing.d.o' 'biod_test@exe/bio_bam_bai_bin.d.o'
'biod_test@exe/bio_bam_multireader.d.o' 'biod_test@exe/bio_bam_reference.d.o'
'biod_test@exe/bio_bam_md_operation.d.o' 'biod_test@exe/bio_bam_md_core.d.o'
'biod_test@exe/bio_bam_md_parse.d.o' 'biod_test@exe/bio_bam_md_reconstruct.d.o'
'biod_test@exe/bio_bam_tagvalue.d.o'
'biod_test@exe/bio_bam_validation_alignment.d.o'
'biod_test@exe/bio_bam_validation_samheader.d.o'
'biod_test@exe/bio_bam_region.d.o'
'biod_test@exe/bio_bam_randomaccessmanager.d.o'
'biod_test@exe/bio_bam_referenceinfo.d.o' 'biod_test@exe/bio_bam_constants.d.o'
'biod_test@exe/bio_bam_snpcallers_maq.d.o'
'biod_test@exe/bio_bam_snpcallers_simple.d.o' 'biod_test@exe/bio_bam_read.d.o'
'biod_test@exe/bio_bam_writer.d.o' 'biod_test@exe/bio_bam_baseinfo.d.o'
'biod_test@exe/bio_maf_reader.d.o' 'biod_test@exe/bio_maf_parser.d.o'
'biod_test@exe/bio_maf_block.d.o' 'biod_test@exe/bio_core_utils_memoize.d.o'
'biod_test@exe/bio_core_utils_algo.d.o'
'biod_test@exe/bio_core_utils_stream.d.o'
'biod_test@exe/bio_core_utils_zlib.d.o'
'biod_test@exe/bio_core_utils_tmpfile.d.o'
'biod_test@exe/bio_core_utils_roundbuf.d.o'
'biod_test@exe/bio_core_utils_format.d.o'
'biod_test@exe/bio_core_utils_bylinefast.d.o'
'biod_test@exe/bio_core_utils_range.d.o'
'biod_test@exe/bio_core_utils_switchendianness.d.o'
'biod_test@exe/bio_core_utils_outbuffer.d.o'
'biod_test@exe/bio_core_genotype.d.o' 'biod_test@exe/bio_core_fasta.d.o'
'biod_test@exe/bio_core_base.d.o' 'biod_test@exe/bio_core_kmer.d.o'
'biod_test@exe/bio_core_region.d.o' 'biod_test@exe/bio_core_tinymap.d.o'
'biod_test@exe/bio_core_sequence.d.o'
'biod_test@exe/bio_core_bgzf_outputstream.d.o'
'biod_test@exe/bio_core_bgzf_chunk.d.o'
'biod_test@exe/bio_core_bgzf_inputstream.d.o'
'biod_test@exe/bio_core_bgzf_constants.d.o'
'biod_test@exe/bio_core_bgzf_block.d.o'
'biod_test@exe/bio_core_bgzf_virtualoffset.d.o'
'biod_test@exe/bio_core_bgzf_compress.d.o' 'biod_test@exe/bio_core_call.d.o'
'biod_test@exe/bio_sff_utils_roundup.d.o' 'biod_test@exe/bio_sff_index.d.o'
'biod_test@exe/bio_sff_readrange.d.o' 'biod_test@exe/bio_sff_reader.d.o'
'biod_test@exe/bio_sff_constants.d.o' 'biod_test@exe/bio_sff_read.d.o'
'biod_test@exe/bio_sff_writer.d.o'
'biod_test@exe/bio_sam_utils_fastrecordparser.d.o'
'biod_test@exe/bio_sam_utils_recordparser.d.o'
'biod_test@exe/bio_sam_reader.d.o' 'biod_test@exe/bio_sam_header.d.o' -O -g
-release -L-z -Lrelro -L-z -Lnow -L-lundead -L-lz
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi':
(.text._D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi[_D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi]+0x11f2):
undefined reference to `_D3std3utf7toUTF16FNaNfxAaZAyu'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi':
(.text._D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi[_D6undead6stream6Stream6vreadfMFAC8TypeInfoPS6object13__va_list_tagZi]+0x1213):
undefined reference to `_D3std3utf7toUTF32FNaNfxAaZAyw'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv':
(.text._D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv[_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv]+0x540):
undefined reference to `_D3std3utf6toUTF8FNaNfxAuZAya'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv':
(.text._D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv[_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZv]+0x5bf):
undefined reference to `_D3std3utf6toUTF8FNaNfxAwZAya'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv':
(.text._D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv[_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv]+0x11a3):
undefined reference to `_D3std3utf6toUTF8FNaNfxAwZAya'
/usr/lib/gcc/x86_64-linux-gnu/6/../../../x86_64-linux-gnu/libundead.a(src_undead_stream.d.o):
In function
`_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv':
(.text._D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv[_D6undead8doformat13__T8doFormatZ8doFormatFMDFwZvAC8TypeInfoPS6object13__va_list_tagZ9formatArgMFaZv]+0x128a):
undefined reference to `_D3std3utf6toUTF8FNaNfxAuZAya'
collect2: error: ld returned 1 exit status
Error: /usr/bin/gcc failed with status: 1
ninja: build stopped: subcommand failed.
debian/rules:20: recipe for target 'override_dh_auto_build' failed
make[1]: *** [override_dh_auto_build] Error 1
make[1]: Leaving directory '/build/libbiod-0.1.0'
debian/rules:13: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
[0mI: copying local configuration[0m
[0;31mE: Failed autobuilding of package[0m
[0mI: unmounting dev/pts filesystem[0m
[0mI: unmounting dev/shm filesystem[0m
[0mI: unmounting proc filesystem[0m
[0mI: unmounting sys filesystem[0m
[0mI: cleaning the build env [0m
[0mI: removing directory /tmp/build/2177 and its subdirectories[0m
signature.asc
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--- End Message ---
--- Begin Message ---
Source: libbiod
Source-Version: 0.1.0-4
We believe that the bug you reported is fixed in the latest version of
libbiod, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 868...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Matthias Klumpp <m...@debian.org> (supplier of updated libbiod package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 04 Aug 2017 12:24:00 -0400
Source: libbiod
Binary: libbiod0 libbiod-dev
Architecture: source amd64
Version: 0.1.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Matthias Klumpp <m...@debian.org>
Description:
libbiod-dev - bioinformatics library in D (development files)
libbiod0 - bioinformatics library in D
Closes: 868455
Changes:
libbiod (0.1.0-4) unstable; urgency=medium
.
* Team upload
* Bump dependency on libundead-dev to build against
shared library version (Closes: #868455)
* Bump standards version: No changes needed
* Use debhelper's built-in Meson support
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Files:
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libbiod0_0.1.0-4_amd64.deb
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libbiod_0.1.0-4_amd64.buildinfo
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