sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +===============================================================================+ | tvc 5.0.3+git20151221.80e144e+dfsg-2 (mipsel) Mon, 18 Mar 2019 10:05:12 +0000 | +===============================================================================+ Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-2 Source Version: 5.0.3+git20151221.80e144e+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: mipsel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-3056affb-b749-43bb-a07c-97955bec938d' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [242 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-03-18-0810.00.pdiff [1538 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-03-18-0810.00.pdiff [1938 B] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-03-18-0810.00.pdiff [1538 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-03-18-0810.00.pdiff [1938 B] Get:6 http://debian.oregonstate.edu/debian unstable/main mipsel Packages [8013 kB] Fetched 8314 kB in 2s (5035 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tvc.git Please use: git clone https://salsa.debian.org/med-team/tvc.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 755 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main tvc 5.0.3+git20151221.80e144e+dfsg-2 (dsc) [2195 B] Get:2 http://debian.oregonstate.edu/debian unstable/main tvc 5.0.3+git20151221.80e144e+dfsg-2 (tar) [745 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main tvc 5.0.3+git20151221.80e144e+dfsg-2 (diff) [8384 B] Fetched 755 kB in 0s (31.5 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/tvc-Pe92Ta/tvc-5.0.3+git20151221.80e144e+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-Pe92Ta' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mipsel:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mipsel:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-SOgqED/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-SOgqED/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SOgqED/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-SOgqED/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SOgqED/apt_archive ./ Sources [363 B] Get:5 copy:/<>/resolver-SOgqED/apt_archive ./ Packages [452 B] Fetched 1772 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: binutils-mipsel-linux-gnu cpp-8-mipsel-linux-gnu cpp-mipsel-linux-gnu cross-config crossbuild-essential-mipsel dpkg-cross file g++-8-mipsel-linux-gnu g++-mipsel-linux-gnu gcc-8-cross-base gcc-8-mipsel-linux-gnu gcc-8-mipsel-linux-gnu-base gcc-mipsel-linux-gnu libatomic1-mipsel-cross libc6-dev-mipsel-cross libc6-mipsel-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mipsel-cross libgcc1-mipsel-cross libgomp1-mipsel-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mipsel-cross libstdc++6-mipsel-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mipsel-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch g++-8-multilib-mipsel-linux-gnu gcc-8-doc libstdc++6-8-dbg-mipsel-cross gcc-8-multilib-mipsel-linux-gnu libgcc1-dbg-mipsel-cross libgomp1-dbg-mipsel-cross libitm1-dbg-mipsel-cross libatomic1-dbg-mipsel-cross libasan5-dbg-mipsel-cross liblsan0-dbg-mipsel-cross libtsan0-dbg-mipsel-cross libubsan1-dbg-mipsel-cross libmpx2-dbg-mipsel-cross libquadmath0-dbg-mipsel-cross manpages-dev autoconf automake libtool flex bison gdb-mipsel-linux-gnu gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-mipsel-linux-gnu cpp-8-mipsel-linux-gnu cpp-mipsel-linux-gnu cross-config crossbuild-essential-mipsel dpkg-cross file g++-8-mipsel-linux-gnu g++-mipsel-linux-gnu gcc-8-cross-base gcc-8-mipsel-linux-gnu gcc-8-mipsel-linux-gnu-base gcc-mipsel-linux-gnu libatomic1-mipsel-cross libc6-dev-mipsel-cross libc6-mipsel-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mipsel-cross libgcc1-mipsel-cross libgomp1-mipsel-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mipsel-cross libstdc++6-mipsel-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mipsel-cross sbuild-build-depends-core-dummy:mipsel sensible-utils ucf 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 40.0 MB of archives. After this operation, 146 MB of additional disk space will be used. Get:1 copy:/<>/resolver-SOgqED/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [872 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-4 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-mipsel-linux-gnu amd64 2.31.1-15 [2490 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mipsel-linux-gnu-base amd64 8.3.0-2cross1 [190 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-mipsel-linux-gnu amd64 8.3.0-2cross1 [6282 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-mipsel-linux-gnu amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-2 [39.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-2cross1 [185 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-mipsel-cross all 2.28-7cross1 [1229 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-mipsel-cross all 1:8.3.0-2cross1 [46.1 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-mipsel-cross all 8.3.0-2cross1 [69.6 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-mipsel-cross all 8.3.0-2cross1 [6688 B] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-mipsel-cross all 8.3.0-2cross1 [211 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mipsel-linux-gnu amd64 8.3.0-2cross1 [6689 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-mipsel-linux-gnu amd64 4:8.3.0-1 [1452 B] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-mipsel-cross all 8.3.0-2cross1 [311 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-mipsel-cross all 4.19.20-1cross1 [1223 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-mipsel-cross all 2.28-7cross1 [2317 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-mipsel-cross all 8.3.0-2cross1 [1535 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-mipsel-linux-gnu amd64 8.3.0-2cross1 [6855 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 g++-mipsel-linux-gnu amd64 4:8.3.0-1 [1172 B] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.1-6 [8292 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-2 [38.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-2 [49.3 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-mipsel all 12.6 [6564 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.0 MB in 0s (81.4 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11931 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4_amd64.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package binutils-mipsel-linux-gnu. Preparing to unpack .../06-binutils-mipsel-linux-gnu_2.31.1-15_amd64.deb ... Unpacking binutils-mipsel-linux-gnu (2.31.1-15) ... Selecting previously unselected package gcc-8-mipsel-linux-gnu-base:amd64. Preparing to unpack .../07-gcc-8-mipsel-linux-gnu-base_8.3.0-2cross1_amd64.deb ... Unpacking gcc-8-mipsel-linux-gnu-base:amd64 (8.3.0-2cross1) ... Selecting previously unselected package cpp-8-mipsel-linux-gnu. Preparing to unpack .../08-cpp-8-mipsel-linux-gnu_8.3.0-2cross1_amd64.deb ... Unpacking cpp-8-mipsel-linux-gnu (8.3.0-2cross1) ... Selecting previously unselected package cpp-mipsel-linux-gnu. Preparing to unpack .../09-cpp-mipsel-linux-gnu_4%3a8.3.0-1_amd64.deb ... Unpacking cpp-mipsel-linux-gnu (4:8.3.0-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../10-cross-config_2.6.15-2_all.deb ... Unpacking cross-config (2.6.15-2) ... 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Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../32-libxml-libxml-perl_2.0134+dfsg-1_amd64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../33-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../34-libyaml-perl_1.27-1_all.deb ... Unpacking libyaml-perl (1.27-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../35-libconfig-auto-perl_0.44-1_all.deb ... Unpacking libconfig-auto-perl (0.44-1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../36-libfile-which-perl_1.23-1_all.deb ... Unpacking libfile-which-perl (1.23-1) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../37-libfile-homedir-perl_1.004-1_all.deb ... Unpacking libfile-homedir-perl (1.004-1) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../38-libdebian-dpkgcross-perl_2.6.15-2_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.15-2) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../39-dpkg-cross_2.6.15-2_all.deb ... Unpacking dpkg-cross (2.6.15-2) ... Selecting previously unselected package crossbuild-essential-mipsel. Preparing to unpack .../40-crossbuild-essential-mipsel_12.6_all.deb ... Unpacking crossbuild-essential-mipsel (12.6) ... Selecting previously unselected package sbuild-build-depends-core-dummy:mipsel. Preparing to unpack .../41-sbuild-build-depends-core-dummy_0.invalid.0_mipsel.deb ... Unpacking sbuild-build-depends-core-dummy:mipsel (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up gcc-8-cross-base (8.3.0-2cross1) ... Setting up libmagic1:amd64 (1:5.35-4) ... Setting up libc6-mipsel-cross (2.28-7cross1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up libatomic1-mipsel-cross (8.3.0-2cross1) ... Setting up file (1:5.35-4) ... Setting up libyaml-perl (1.27-1) ... Setting up libicu63:amd64 (63.1-6) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-2) ... Setting up libgcc1-mipsel-cross (1:8.3.0-2cross1) ... Setting up binutils-mipsel-linux-gnu (2.31.1-15) ... Setting up libgomp1-mipsel-cross (8.3.0-2cross1) ... Setting up gcc-8-mipsel-linux-gnu-base:amd64 (8.3.0-2cross1) ... Setting up linux-libc-dev-mipsel-cross (4.19.20-1cross1) ... Setting up sensible-utils (0.0.12) ... Setting up cpp-8-mipsel-linux-gnu (8.3.0-2cross1) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libgcc-8-dev-mipsel-cross (8.3.0-2cross1) ... Setting up libc6-dev-mipsel-cross (2.28-7cross1) ... Setting up libstdc++6-mipsel-cross (8.3.0-2cross1) ... Setting up cpp-mipsel-linux-gnu (4:8.3.0-1) ... Setting up ucf (3.0038+nmu1) ... Setting up libstdc++-8-dev-mipsel-cross (8.3.0-2cross1) ... Setting up gcc-8-mipsel-linux-gnu (8.3.0-2cross1) ... Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-mipsel-linux-gnu (4:8.3.0-1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up g++-8-mipsel-linux-gnu (8.3.0-2cross1) ... Setting up g++-mipsel-linux-gnu (4:8.3.0-1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-2) ... Setting up dpkg-cross (2.6.15-2) ... Setting up crossbuild-essential-mipsel (12.6) ... Setting up sbuild-build-depends-core-dummy:mipsel (0.invalid.0) ... Processing triggers for libc-bin (2.28-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (mipsel included in any) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-SOgqED/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-SOgqED/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SOgqED/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-SOgqED/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SOgqED/apt_archive ./ Sources [482 B] Get:5 copy:/<>/resolver-SOgqED/apt_archive ./ Packages [570 B] Fetched 2015 B in 0s (0 B/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:mipsel 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 840 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-SOgqED/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 840 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:mipsel. (Reading database ... 15102 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_mipsel.deb ... Unpacking sbuild-build-depends-essential-dummy:mipsel (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:mipsel (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev dpkg-deb: building package 'sbuild-build-depends-tvc-dummy' in '/<>/resolver-SOgqED/apt_archive/sbuild-build-depends-tvc-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-tvc-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-SOgqED/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SOgqED/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-SOgqED/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SOgqED/apt_archive ./ Sources [676 B] Get:5 copy:/<>/resolver-SOgqED/apt_archive ./ Packages [760 B] Fetched 2399 B in 0s (151 kB/s) Reading package lists... Reading package lists... Install tvc build dependencies (apt-based resolver) --------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:mipsel gettext gettext-base groff-base hdf5-helpers:mipsel intltool-debian libaec-dev:mipsel libaec0:mipsel libarchive-zip-perl libarchive13 libarmadillo-dev:mipsel libarmadillo9:mipsel libarpack2:mipsel libarpack2-dev:mipsel libatomic1:mipsel libbamtools-dev:mipsel libbamtools2.5.1:mipsel libblas-dev:mipsel libblas3:mipsel libboost-math-dev:mipsel libboost-math1.67-dev:mipsel libboost-math1.67.0:mipsel libboost1.67-dev:mipsel libbsd0 libc6:mipsel libc6-dev:mipsel libcroco3 libcurl4 libdisorder-dev:mipsel libdisorder0:mipsel libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-8-dev:mipsel libgcc1:mipsel libgfortran5:mipsel libglib2.0-0 libgomp1:mipsel libgssapi-krb5-2 libhdf5-103:mipsel libhdf5-cpp-103:mipsel libhdf5-dev:mipsel libjpeg62-turbo:mipsel libjpeg62-turbo-dev:mipsel libjsoncpp-dev:mipsel libjsoncpp1 libjsoncpp1:mipsel libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:mipsel liblapack3:mipsel libldap-2.4-2 libldap-common libncurses6 libnghttp2-14 libpipeline1 libprocps7 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:mipsel libsmithwaterman0:mipsel libssh2-1 libssl1.1 libstdc++-8-dev:mipsel libstdc++6:mipsel libsuperlu-dev:mipsel libsuperlu5:mipsel libsz2:mipsel libtool libuchardet0 libuv1 linux-libc-dev:mipsel lsb-base m4 man-db po-debconf procps zlib1g:mipsel zlib1g-dev:mipsel Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libitpp-dev:mipsel libbamtools-doc:mipsel liblapack-doc:mipsel libboost1.67-doc:mipsel libboost-atomic1.67-dev:mipsel libboost-chrono1.67-dev:mipsel libboost-container1.67-dev:mipsel libboost-context1.67-dev:mipsel libboost-coroutine1.67-dev:mipsel libboost-date-time1.67-dev:mipsel libboost-exception1.67-dev:mipsel libboost-fiber1.67-dev:mipsel libboost-filesystem1.67-dev:mipsel libboost-graph1.67-dev:mipsel libboost-graph-parallel1.67-dev:mipsel libboost-iostreams1.67-dev:mipsel libboost-locale1.67-dev:mipsel libboost-log1.67-dev:mipsel libboost-mpi1.67-dev:mipsel libboost-mpi-python1.67-dev:mipsel libboost-numpy1.67-dev:mipsel libboost-program-options1.67-dev:mipsel libboost-python1.67-dev:mipsel libboost-random1.67-dev:mipsel libboost-regex1.67-dev:mipsel libboost-serialization1.67-dev:mipsel libboost-signals1.67-dev:mipsel libboost-stacktrace1.67-dev:mipsel libboost-system1.67-dev:mipsel libboost-test1.67-dev:mipsel libboost-thread1.67-dev:mipsel libboost-timer1.67-dev:mipsel libboost-type-erasure1.67-dev:mipsel libboost-wave1.67-dev:mipsel libboost1.67-tools-dev:mipsel libmpfrc++-dev:mipsel libntl-dev:mipsel glibc-doc:mipsel libc-l10n:mipsel locales:mipsel manpages-dev:mipsel krb5-doc krb5-user libhdf5-doc:mipsel libstdc++-8-doc:mipsel libsuperlu-doc:mipsel libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:mipsel ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:mipsel gettext gettext-base groff-base hdf5-helpers:mipsel intltool-debian libaec-dev:mipsel libaec0:mipsel libarchive-zip-perl libarchive13 libarmadillo-dev:mipsel libarmadillo9:mipsel libarpack2:mipsel libarpack2-dev:mipsel libatomic1:mipsel libbamtools-dev:mipsel libbamtools2.5.1:mipsel libblas-dev:mipsel libblas3:mipsel libboost-math-dev:mipsel libboost-math1.67-dev:mipsel libboost-math1.67.0:mipsel libboost1.67-dev:mipsel libbsd0 libc6:mipsel libc6-dev:mipsel libcroco3 libcurl4 libdisorder-dev:mipsel libdisorder0:mipsel libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-8-dev:mipsel libgcc1:mipsel libgfortran5:mipsel libglib2.0-0 libgomp1:mipsel libgssapi-krb5-2 libhdf5-103:mipsel libhdf5-cpp-103:mipsel libhdf5-dev:mipsel libjpeg62-turbo:mipsel libjpeg62-turbo-dev:mipsel libjsoncpp-dev:mipsel libjsoncpp1 libjsoncpp1:mipsel libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:mipsel liblapack3:mipsel libldap-2.4-2 libldap-common libncurses6 libnghttp2-14 libpipeline1 libprocps7 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:mipsel libsmithwaterman0:mipsel libssh2-1 libssl1.1 libstdc++-8-dev:mipsel libstdc++6:mipsel libsuperlu-dev:mipsel libsuperlu5:mipsel libsz2:mipsel libtool libuchardet0 libuv1 linux-libc-dev:mipsel lsb-base m4 man-db po-debconf procps sbuild-build-depends-tvc-dummy:mipsel zlib1g:mipsel zlib1g-dev:mipsel 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 47.1 MB of archives. After this operation, 303 MB of additional disk space will be used. Get:1 copy:/<>/resolver-SOgqED/apt_archive ./ sbuild-build-depends-tvc-dummy 0.invalid.0 [920 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 lsb-base all 10.2019031300 [28.3 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive13 amd64 3.3.3-4 [314 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5support0 amd64 1.17-2 [65.6 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libk5crypto3 amd64 1.17-2 [121 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1b-1 [1531 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5-3 amd64 1.17-2 [368 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-2 [158 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1 [69.0 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1 [106 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-common all 2.4.47+dfsg-3 [89.4 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3 [224 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libnghttp2-14 amd64 1.37.0-1 [83.3 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libssh2-1 amd64 1.8.0-2 [138 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libcurl4 amd64 7.64.0-2 [331 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.6-1 [105 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libuv1 amd64 1.24.1-1 [110 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1 [160 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-1 [1258 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main mipsel gcc-8-base mipsel 8.3.0-3 [190 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main mipsel hdf5-helpers mipsel 1.10.4+repack-10 [35.2 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main mipsel libgcc1 mipsel 1:8.3.0-3 [46.0 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main mipsel libc6 mipsel 2.28-8 [2424 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main mipsel libaec0 mipsel 1.0.2-1 [20.8 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main mipsel libsz2 mipsel 1.0.2-1 [6576 B] Get:60 http://debian.oregonstate.edu/debian unstable/main mipsel libaec-dev mipsel 1.0.2-1 [19.8 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main mipsel zlib1g mipsel 1:1.2.11.dfsg-1 [90.3 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main mipsel libgfortran5 mipsel 8.3.0-3 [233 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main mipsel libblas3 mipsel 3.8.0-2 [134 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main mipsel liblapack3 mipsel 3.8.0-2 [1963 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main mipsel libarpack2 mipsel 3.7.0-1 [95.5 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main mipsel libstdc++6 mipsel 8.3.0-3 [348 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main mipsel libsuperlu5 mipsel 5.2.1+dfsg1-4 [137 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main mipsel libarmadillo9 mipsel 1:9.200.7+dfsg-1 [88.1 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main mipsel libblas-dev mipsel 3.8.0-2 [153 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main mipsel liblapack-dev mipsel 3.8.0-2 [2230 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main mipsel libarpack2-dev mipsel 3.7.0-1 [123 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main mipsel libhdf5-103 mipsel 1.10.4+repack-10 [1020 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main mipsel linux-libc-dev mipsel 4.19.28-2 [1152 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main mipsel libc6-dev mipsel 2.28-8 [2322 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main mipsel zlib1g-dev mipsel 1:1.2.11.dfsg-1 [213 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main mipsel libjpeg62-turbo mipsel 1:1.5.2-2+b1 [127 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main mipsel libjpeg62-turbo-dev mipsel 1:1.5.2-2+b1 [203 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main mipsel libhdf5-cpp-103 mipsel 1.10.4+repack-10 [123 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main mipsel libhdf5-dev mipsel 1.10.4+repack-10 [2662 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main mipsel libsuperlu-dev mipsel 5.2.1+dfsg1-4 [18.4 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main mipsel libarmadillo-dev mipsel 1:9.200.7+dfsg-1 [360 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main mipsel libatomic1 mipsel 8.3.0-3 [6700 B] Get:83 http://debian.oregonstate.edu/debian unstable/main mipsel libbamtools2.5.1 mipsel 2.5.1+dfsg-3 [141 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main mipsel libbamtools-dev mipsel 2.5.1+dfsg-3 [21.8 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main mipsel libgomp1 mipsel 8.3.0-3 [70.9 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main mipsel libgcc-8-dev mipsel 8.3.0-3 [210 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main mipsel libstdc++-8-dev mipsel 8.3.0-3 [1553 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main mipsel libboost1.67-dev mipsel 1.67.0-13 [8386 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main mipsel libboost-math1.67.0 mipsel 1.67.0-13 [339 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main mipsel libboost-math1.67-dev mipsel 1.67.0-13 [536 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main mipsel libboost-math-dev mipsel 1.67.0.1 [3852 B] Get:92 http://debian.oregonstate.edu/debian unstable/main mipsel libdisorder0 mipsel 0.0.2+git20130809.8062ee1-1 [4472 B] Get:93 http://debian.oregonstate.edu/debian unstable/main mipsel libdisorder-dev mipsel 0.0.2+git20130809.8062ee1-1 [4396 B] Get:94 http://debian.oregonstate.edu/debian unstable/main mipsel libjsoncpp1 mipsel 1.7.4-3 [73.1 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main mipsel libjsoncpp-dev mipsel 1.7.4-3 [96.5 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main mipsel libsmithwaterman0 mipsel 0.0+git20160702.2610e25-7 [32.9 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main mipsel libsmithwaterman-dev mipsel 0.0+git20160702.2610e25-7 [40.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.1 MB in 1s (32.5 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15102 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libncurses6:amd64. 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Setting up librhash0:amd64 (1.3.8-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libssh2-1:amd64 (1.8.0-2) ... Setting up cmake-data (3.13.4-1) ... Setting up libkrb5-3:amd64 (1.17-2) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-2) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libcurl4:amd64 (7.64.0-2) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up cmake (3.13.4-1) ... Setting up dh-autoreconf (19) ... Setting up libc6:mipsel (2.28-8) ... Setting up libc6-dev:mipsel (2.28-8) ... Setting up libdisorder0:mipsel (0.0.2+git20130809.8062ee1-1) ... Setting up libgcc1:mipsel (1:8.3.0-3) ... Setting up debhelper (12.1.1) ... Setting up zlib1g:mipsel (1:1.2.11.dfsg-1) ... Setting up libgomp1:mipsel (8.3.0-3) ... Setting up libaec0:mipsel (1.0.2-1) ... Setting up libjpeg62-turbo:mipsel (1:1.5.2-2+b1) ... Setting up libjpeg62-turbo-dev:mipsel (1:1.5.2-2+b1) ... Setting up libatomic1:mipsel (8.3.0-3) ... Setting up libdisorder-dev:mipsel (0.0.2+git20130809.8062ee1-1) ... Setting up libgcc-8-dev:mipsel (8.3.0-3) ... Setting up libgfortran5:mipsel (8.3.0-3) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up zlib1g-dev:mipsel (1:1.2.11.dfsg-1) ... Setting up libstdc++6:mipsel (8.3.0-3) ... Setting up libsz2:mipsel (1.0.2-1) ... Setting up libjsoncpp1:mipsel (1.7.4-3) ... Setting up libstdc++-8-dev:mipsel (8.3.0-3) ... Setting up libboost1.67-dev:mipsel (1.67.0-13) ... Setting up libjsoncpp-dev:mipsel (1.7.4-3) ... Setting up libaec-dev:mipsel (1.0.2-1) ... Setting up libsmithwaterman0:mipsel (0.0+git20160702.2610e25-7) ... Setting up libboost-math1.67.0:mipsel (1.67.0-13) ... Setting up libblas3:mipsel (3.8.0-2) ... update-alternatives: using /usr/lib/mipsel-linux-gnu/blas/libblas.so.3 to provide /usr/lib/mipsel-linux-gnu/libblas.so.3 (libblas.so.3-mipsel-linux-gnu) in auto mode Setting up libhdf5-103:mipsel (1.10.4+repack-10) ... Setting up libbamtools2.5.1:mipsel (2.5.1+dfsg-3) ... Setting up libsmithwaterman-dev:mipsel (0.0+git20160702.2610e25-7) ... Setting up libblas-dev:mipsel (3.8.0-2) ... update-alternatives: using /usr/lib/mipsel-linux-gnu/blas/libblas.so to provide /usr/lib/mipsel-linux-gnu/libblas.so (libblas.so-mipsel-linux-gnu) in auto mode Setting up liblapack3:mipsel (3.8.0-2) ... update-alternatives: using /usr/lib/mipsel-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/mipsel-linux-gnu/liblapack.so.3 (liblapack.so.3-mipsel-linux-gnu) in auto mode Setting up libboost-math1.67-dev:mipsel (1.67.0-13) ... Setting up libboost-math-dev:mipsel (1.67.0.1) ... Setting up libhdf5-cpp-103:mipsel (1.10.4+repack-10) ... Setting up libarpack2:mipsel (3.7.0-1) ... Setting up libsuperlu5:mipsel (5.2.1+dfsg1-4) ... Setting up libbamtools-dev:mipsel (2.5.1+dfsg-3) ... Setting up libhdf5-dev:mipsel (1.10.4+repack-10) ... update-alternatives: using /usr/lib/mipsel-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/mipsel-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up liblapack-dev:mipsel (3.8.0-2) ... update-alternatives: using /usr/lib/mipsel-linux-gnu/lapack/liblapack.so to provide /usr/lib/mipsel-linux-gnu/liblapack.so (liblapack.so-mipsel-linux-gnu) in auto mode Setting up libarmadillo9:mipsel (1:9.200.7+dfsg-1) ... Setting up libsuperlu-dev:mipsel (5.2.1+dfsg1-4) ... Setting up libarpack2-dev:mipsel (3.7.0-1) ... Setting up libarmadillo-dev:mipsel (1:9.200.7+dfsg-1) ... Setting up sbuild-build-depends-tvc-dummy:mipsel (0.invalid.0) ... Processing triggers for libc-bin (2.28-8) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-15 dpkg-dev_1.19.5 g++-8_8.3.0-3 gcc-8_8.3.0-3 libc6-dev_2.28-8 libstdc++-8-dev_8.3.0-3 libstdc++-8-dev-mipsel-cross_8.3.0-2cross1 libstdc++6_8.3.0-3 libstdc++6-mipsel-cross_8.3.0-2cross1 linux-libc-dev_4.19.28-2 Package versions: adduser_3.118 apt_1.8.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.46 bash_5.0-2 binutils_2.31.1-15 binutils-common_2.31.1-15 binutils-mipsel-linux-gnu_2.31.1-15 binutils-x86-64-linux-gnu_2.31.1-15 bsdmainutils_11.1.2+b1 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9 cmake_3.13.4-1 cmake-data_3.13.4-1 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-8_8.3.0-3 cpp-8-mipsel-linux-gnu_8.3.0-2cross1 cpp-mipsel-linux-gnu_4:8.3.0-1 cross-config_2.6.15-2 crossbuild-essential-mipsel_12.6 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.1.1 debian-archive-keyring_2018.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-2 dpkg_1.19.5 dpkg-cross_2.6.15-2 dpkg-dev_1.19.5 dwz_0.12-3 e2fsprogs_1.45.0-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1 g++-8_8.3.0-3 g++-8-mipsel-linux-gnu_8.3.0-2cross1 g++-mipsel-linux-gnu_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-3 gcc-8-base_8.3.0-3 gcc-8-cross-base_8.3.0-2cross1 gcc-8-mipsel-linux-gnu_8.3.0-2cross1 gcc-8-mipsel-linux-gnu-base_8.3.0-2cross1 gcc-mipsel-linux-gnu_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.13-1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hdf5-helpers_1.10.4+repack-10 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapt-pkg5.0_1.8.0 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-4 libarmadillo-dev_1:9.200.7+dfsg-1 libarmadillo9_1:9.200.7+dfsg-1 libarpack2_3.7.0-1 libarpack2-dev_3.7.0-1 libasan5_8.3.0-3 libatomic1_8.3.0-3 libatomic1-mipsel-cross_8.3.0-2cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.31.1-15 libblas-dev_3.8.0-2 libblas3_3.8.0-2 libblkid1_2.33.1-0.1 libboost-math-dev_1.67.0.1 libboost-math1.67-dev_1.67.0-13 libboost-math1.67.0_1.67.0-13 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9 libc-bin_2.28-8 libc-dev-bin_2.28-8 libc6_2.28-8 libc6-dev_2.28-8 libc6-dev-mipsel-cross_2.28-7cross1 libc6-mipsel-cross_2.28-7cross1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-3 libcom-err2_1.45.0-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libcurl4_7.64.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.248 libdebian-dpkgcross-perl_2.6.15-2 libdisorder-dev_0.0.2+git20130809.8062ee1-1 libdisorder0_0.0.2+git20130809.8062ee1-1 libdpkg-perl_1.19.5 libelf1_0.176-1 libexpat1_2.2.6-1 libext2fs2_1.45.0-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.1.2-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-3 libgcc-8-dev-mipsel-cross_8.3.0-2cross1 libgcc1_1:8.3.0-3 libgcc1-mipsel-cross_1:8.3.0-2cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libgfortran5_8.3.0-3 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-3 libgomp1_8.3.0-3 libgomp1-mipsel-cross_8.3.0-2cross1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-2 libhdf5-103_1.10.4+repack-10 libhdf5-cpp-103_1.10.4+repack-10 libhdf5-dev_1.10.4+repack-10 libhogweed4_3.4.1-1 libicu63_63.1-6 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.3.0-3 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjsoncpp-dev_1.7.4-3 libjsoncpp1_1.7.4-3 libk5crypto3_1.17-2 libkeyutils1_1.6-6 libkrb5-3_1.17-2 libkrb5support0_1.17-2 liblapack-dev_3.8.0-2 liblapack3_3.8.0-2 libldap-2.4-2_2.4.47+dfsg-3 libldap-common_2.4.47+dfsg-3 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.3.0-3 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-3 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.37.0-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-5 libpipeline1_1.5.1-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libquadmath0_8.3.0-3 librhash0_1.3.8-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsmithwaterman-dev_0.0+git20160702.2610e25-7 libsmithwaterman0_0.0+git20160702.2610e25-7 libss2_1.45.0-1 libssh2-1_1.8.0-2 libssl1.1_1.1.1b-1 libstdc++-8-dev_8.3.0-3 libstdc++-8-dev-mipsel-cross_8.3.0-2cross1 libstdc++6_8.3.0-3 libstdc++6-mipsel-cross_8.3.0-2cross1 libsuperlu-dev_5.2.1+dfsg1-4 libsuperlu5_5.2.1+dfsg1-4 libsystemd0_241-2 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-3 libubsan1_8.3.0-3 libuchardet0_0.0.6-3 libudev1_241-2 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libuv1_1.24.1-1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.28-2 linux-libc-dev-mipsel-cross_4.19.20-1cross1 login_1:4.5-1.1 lsb-base_10.2019031300 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17+b3 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-5 perl-base_5.28.1-5 perl-modules-5.28_5.28.1-5 po-debconf_1.0.21 procps_2:3.3.15-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-tvc-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-5 tzdata_2018i-2 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Dec 13 07:20:19 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tvc_5.0.3+git20151221.80e144e+dfsg-2.dsc dpkg-source: info: extracting tvc in /<>/tvc-5.0.3+git20151221.80e144e+dfsg dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cmake.patch dpkg-source: info: applying bamtools.patch dpkg-source: info: applying help.patch dpkg-source: info: applying hurd.patch dpkg-source: info: applying sse.patch dpkg-source: info: applying use_debian_packaged_smithwaterman.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.mipsel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-3056affb-b749-43bb-a07c-97955bec938d SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type mipsel-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture mipsel fakeroot debian/rules clean dh clean dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-mipsel-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=mipsel -DCMAKE_C_COMPILER=mipsel-linux-gnu-gcc -DCMAKE_CXX_COMPILER=mipsel-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/mipsel-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/mipsel-linux-gnu-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/mipsel-linux-gnu-qmake -DCMAKE_INSTALL_LIBDIR=lib/mipsel-linux-gnu .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mipsel-linux-gnu-gcc -- Check for working C compiler: /usr/bin/mipsel-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mipsel-linux-gnu-g++ -- Check for working CXX compiler: /usr/bin/mipsel-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE QMAKE_EXECUTABLE -- Build files have been written to: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu dh_auto_build -a cd obj-mipsel-linux-gnu && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mipsel-linux-gnu-pkg-config CXX=mipsel-linux-gnu-g\+\+ CC=mipsel-linux-gnu-gcc make[1]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' /usr/bin/cmake -S/<>/tvc-5.0.3+git20151221.80e144e+dfsg -B/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= Scanning dependencies of target tvcassembly make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' [ 1%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/IndelAssembly/IndelAssembly.cpp [ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp [ 4%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp [ 6%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 7%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/Utils.cpp [ 9%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/IonVersion.cpp [ 10%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/mipsel-linux-gnu-g++ -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -o tvcassembly -lbamtools -lz -lpthread -ljsoncpp make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' [ 10%] Built target tvcassembly make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= Scanning dependencies of target tvc make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' [ 12%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:9: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err1(null_ostream); ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:353, from /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here set_stream_err1(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:37: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err1(null_ostream); ^ In file included from /usr/include/armadillo:353, from /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here set_stream_err1(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:37: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err1(null_ostream); ^ In file included from /usr/include/armadillo:353, from /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here set_stream_err1(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:9: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(null_ostream); ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:353, from /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here set_stream_err2(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:37: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(null_ostream); ^ In file included from /usr/include/armadillo:353, from /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here set_stream_err2(std::ostream& user_stream) ^~~~~~~~~~~~~~~ /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:37: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations] arma::set_stream_err2(null_ostream); ^ In file included from /usr/include/armadillo:353, from /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here set_stream_err2(std::ostream& user_stream) ^~~~~~~~~~~~~~~ [ 14%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/BAMWalkerEngine.cpp [ 15%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads 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/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp [ 18%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp [ 20%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping 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-I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp [ 29%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller 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CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads/ExtendedReadInfo.cpp [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ErrorMotifs.cpp [ 34%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/LocalContext.cpp [ 35%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ClassifyVariant.cpp [ 37%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/SpliceVariantHypotheses.cpp [ 39%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/DecisionTreeData.cpp [ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:22: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(stdout, "ref.size()=%lu; ", ref.size()); ^~~~~~~~~~~~~~~~~~ ~~~~~~~~~~ /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:22: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(stdout, "var.size()=%lu; ", var.size()); ^~~~~~~~~~~~~~~~~~ ~~~~~~~~~~ /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:193:22: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] fprintf(stdout, "both.size()=%lu; ", both.size()); ^~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ [ 42%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HypothesisEvaluator.cpp [ 43%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller 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/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(buf, 1, 28, fp->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter 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-I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 73%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping 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-I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp [ 92%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 93%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp [ 95%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/mipsel-linux-gnu-gcc -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong 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-I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': /<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(buf, 1, 28, fp->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o /usr/bin/mipsel-linux-gnu-g++ -DALIGNSTATS_IGNORE -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/<>/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/IonVersion.cpp [100%] Linking CXX executable tvcutils /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1 /usr/bin/mipsel-linux-gnu-g++ -g -O2 -fdebug-prefix-map=/<>/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' [100%] Built target tvcutils make[2]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a cd obj-mipsel-linux-gnu && make -j1 install DESTDIR=/<>/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' /usr/bin/cmake -S/<>/tvc-5.0.3+git20151221.80e144e+dfsg -B/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' [ 10%] Built target tvcassembly make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' [ 79%] Built target tvc make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' [100%] Built target tvcutils make[2]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /<>/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf make[1]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mipsel-linux-gnu' dh_installdocs -a dh_installchangelogs -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against liblapack.so.3 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils were not linked against libdisorder.so.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc was not linked against libblas.so.3 (it uses none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-2_mipsel.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_mipsel.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../tvc_5.0.3+git20151221.80e144e+dfsg-2_mipsel.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-03-18T10:10:13Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/resolver-SOgqED/apt_archive/sbuild-build-depends-lintian-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-lintian-dummy sbuild-build-depends-tvc-dummy dpkg-scanpackages: info: Wrote 4 entries to output Packages file. Ign:1 copy:/<>/resolver-SOgqED/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SOgqED/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-SOgqED/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SOgqED/apt_archive ./ Sources [796 B] Get:5 copy:/<>/resolver-SOgqED/apt_archive ./ Packages [876 B] Fetched 2635 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline7 libsqlite3-0 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libhtml-template-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline7 libsqlite3-0 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:mipsel t1utils 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. Need to get 6252 kB of archives. After this operation, 16.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-SOgqED/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 7.0-5 [70.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1 [33.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.2-1 [49.4 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.13-1 [512 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.27.2-1 [640 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.13-1 [867 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.34+b1 [71.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.40-1 [222 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.18-1 [88.5 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.19-1 [372 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.39-1 [74.5 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.72-1 [262 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.76+repack-1 [33.1 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2 [90.4 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.10.0 [1195 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6252 kB in 0s (29.2 MB/s) Selecting previously unselected package netbase. (Reading database ... 36101 files and directories currently installed.) Preparing to unpack .../00-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package readline-common. Preparing to unpack .../01-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package diffstat. Preparing to unpack .../02-diffstat_1.62-1_amd64.deb ... Unpacking diffstat (1.62-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../03-libassuan0_2.5.2-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.2-1) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../04-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.13-1_amd64.deb ... Unpacking gpgconf (2.2.13-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../06-libsqlite3-0_3.27.2-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.27.2-1) ... Selecting previously unselected package gpg. Preparing to unpack .../07-gpg_2.2.13-1_amd64.deb ... Unpacking gpg (2.2.13-1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../08-libapt-pkg-perl_0.1.34+b1_amd64.deb ... Unpacking libapt-pkg-perl (0.1.34+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../09-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../10-libhtml-tagset-perl_3.20-3_all.deb ... Unpacking libhtml-tagset-perl (3.20-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../11-liburi-perl_1.76-1_all.deb ... Unpacking liburi-perl (1.76-1) ... Selecting previously unselected package libhtml-parser-perl. Preparing to unpack .../12-libhtml-parser-perl_3.72-3+b3_amd64.deb ... Unpacking libhtml-parser-perl (3.72-3+b3) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../13-libcgi-pm-perl_4.40-1_all.deb ... Unpacking libcgi-pm-perl (4.40-1) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../14-libsub-name-perl_0.21-1+b3_amd64.deb ... Unpacking libsub-name-perl (0.21-1+b3) ... Selecting previously unselected package libclass-accessor-perl. Preparing to unpack .../15-libclass-accessor-perl_0.51-1_all.deb ... Unpacking libclass-accessor-perl (0.51-1) ... Selecting previously unselected package libclone-perl. Preparing to unpack .../16-libclone-perl_0.41-1+b1_amd64.deb ... Unpacking libclone-perl (0.41-1+b1) ... Selecting previously unselected package libdigest-hmac-perl. Preparing to unpack .../17-libdigest-hmac-perl_1.03+dfsg-2_all.deb ... Unpacking libdigest-hmac-perl (1.03+dfsg-2) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../18-libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package perl-openssl-defaults:amd64. Preparing to unpack .../19-perl-openssl-defaults_3_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (3) ... Selecting previously unselected package libnet-ssleay-perl. Preparing to unpack .../20-libnet-ssleay-perl_1.85-2+b1_amd64.deb ... Unpacking libnet-ssleay-perl (1.85-2+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../21-libio-socket-ssl-perl_2.060-3_all.deb ... Unpacking libio-socket-ssl-perl (2.060-3) ... Selecting previously unselected package libnet-smtp-ssl-perl. Preparing to unpack .../22-libnet-smtp-ssl-perl_1.04-1_all.deb ... Unpacking libnet-smtp-ssl-perl (1.04-1) ... Selecting previously unselected package libmailtools-perl. Preparing to unpack .../23-libmailtools-perl_2.18-1_all.deb ... Unpacking libmailtools-perl (2.18-1) ... Selecting previously unselected package libnet-ip-perl. Preparing to unpack .../24-libnet-ip-perl_1.26-2_all.deb ... Unpacking libnet-ip-perl (1.26-2) ... Selecting previously unselected package libnet-dns-perl. Preparing to unpack .../25-libnet-dns-perl_1.19-1_all.deb ... Unpacking libnet-dns-perl (1.19-1) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../26-libnet-domain-tld-perl_1.75-1_all.deb ... Unpacking libnet-domain-tld-perl (1.75-1) ... Selecting previously unselected package libemail-valid-perl. Preparing to unpack .../27-libemail-valid-perl_1.202-1_all.deb ... Unpacking libemail-valid-perl (1.202-1) ... Selecting previously unselected package libexporter-tiny-perl. Preparing to unpack .../28-libexporter-tiny-perl_1.002001-1_all.deb ... Unpacking libexporter-tiny-perl (1.002001-1) ... Selecting previously unselected package libipc-system-simple-perl. 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ tvc_5.0.3+git20151221.80e144e+dfsg-2_mipsel.changes: ---------------------------------------------------- Format: 1.8 Date: Thu, 13 Dec 2018 08:07:07 +0100 Source: tvc Binary: tvc tvc-dbgsym Built-For-Profiles: cross nocheck Architecture: mipsel Version: 5.0.3+git20151221.80e144e+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: tvc - genetic variant caller for Ion Torrent sequencing platforms Closes: 916322 Changes: tvc (5.0.3+git20151221.80e144e+dfsg-2) unstable; urgency=medium . [ Logan Rosen ] * Enable build with ld --as-needed Closes: #916322 . 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1d76a80a63d9becaf46359cefccbb38a9fa158cd6c52b01e1c4c3d1422c25d3e 1001680 tvc_5.0.3+git20151221.80e144e+dfsg-2_mipsel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 18 Mar 2019 10:10:13 +0000 Build-Path: /<>/tvc-5.0.3+git20151221.80e144e+dfsg Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 10.1), base-passwd (= 3.5.46), bash (= 5.0-2), binutils (= 2.31.1-15), binutils-common (= 2.31.1-15), binutils-x86-64-linux-gnu (= 2.31.1-15), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.33.1-0.1), build-essential (= 12.6), bzip2 (= 1.0.6-9), cmake (= 3.13.4-1), cmake-data (= 3.13.4-1), coreutils (= 8.30-3), cpp (= 4:8.3.0-1), cpp-8 (= 8.3.0-3), dash (= 0.5.10.2-5), debconf (= 1.5.71), debhelper (= 12.1.1), debianutils (= 4.8.6.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.1.2-1), diffutils (= 1:3.7-2), dpkg (= 1.19.5), dpkg-dev (= 1.19.5), dwz (= 0.12-3), fdisk (= 2.33.1-0.1), file (= 1:5.35-4), findutils (= 4.6.0+git+20190209-2), g++ (= 4:8.3.0-1), g++-8 (= 8.3.0-3), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-3), gcc-8-base (= 8.3.0-3), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3), hdf5-helpers (= 1.10.4+repack-10), hostname (= 3.21), init-system-helpers (= 1.56+nmu1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-4), libaec-dev (= 1.0.2-1), libaec0 (= 1.0.2-1), libarchive-zip-perl (= 1.64-1), libarchive13 (= 3.3.3-4), libarmadillo-dev (= 1:9.200.7+dfsg-1), libarmadillo9 (= 1:9.200.7+dfsg-1), libarpack2 (= 3.7.0-1), libarpack2-dev (= 3.7.0-1), libasan5 (= 8.3.0-3), libatomic1 (= 8.3.0-3), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.4-2), libaudit1 (= 1:2.8.4-2), libbamtools-dev (= 2.5.1+dfsg-3), libbamtools2.5.1 (= 2.5.1+dfsg-3), libbinutils (= 2.31.1-15), libblas-dev (= 3.8.0-2), libblas3 (= 3.8.0-2), libblkid1 (= 2.33.1-0.1), libboost-math-dev (= 1.67.0.1), libboost-math1.67-dev (= 1.67.0-13), libboost-math1.67.0 (= 1.67.0-13), libboost1.67-dev (= 1.67.0-13), libbsd0 (= 0.9.1-2), libbz2-1.0 (= 1.0.6-9), libc-bin (= 2.28-8), libc-dev-bin (= 2.28-8), libc6 (= 2.28-8), libc6-dev (= 2.28-8), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 8.3.0-3), libcom-err2 (= 1.45.0-1), libcroco3 (= 0.6.12-3), libcurl4 (= 7.64.0-2), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.248), libdisorder-dev (= 0.0.2+git20130809.8062ee1-1), libdisorder0 (= 0.0.2+git20130809.8062ee1-1), libdpkg-perl (= 1.19.5), libelf1 (= 0.176-1), libexpat1 (= 2.2.6-1), libfdisk1 (= 2.33.1-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.1.2-1), libgcc-8-dev (= 8.3.0-3), libgcc1 (= 1:8.3.0-3), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-4), libgdbm6 (= 1.18.1-4), libgfortran5 (= 8.3.0-3), libglib2.0-0 (= 2.58.3-1), libgmp10 (= 2:6.1.2+dfsg-4), libgnutls30 (= 3.6.6-3), libgomp1 (= 8.3.0-3), libgpg-error0 (= 1.35-1), libgssapi-krb5-2 (= 1.17-2), libhdf5-103 (= 1.10.4+repack-10), libhdf5-cpp-103 (= 1.10.4+repack-10), libhdf5-dev (= 1.10.4+repack-10), libhogweed4 (= 3.4.1-1), libicu63 (= 63.1-6), libidn2-0 (= 2.0.5-1), libisl19 (= 0.20-2), libitm1 (= 8.3.0-3), libjpeg62-turbo (= 1:1.5.2-2+b1), libjpeg62-turbo-dev (= 1:1.5.2-2+b1), libjsoncpp-dev (= 1.7.4-3), libjsoncpp1 (= 1.7.4-3), libk5crypto3 (= 1.17-2), libkeyutils1 (= 1.6-6), libkrb5-3 (= 1.17-2), libkrb5support0 (= 1.17-2), liblapack-dev (= 3.8.0-2), liblapack3 (= 3.8.0-2), libldap-2.4-2 (= 2.4.47+dfsg-3), libldap-common (= 2.4.47+dfsg-3), liblsan0 (= 8.3.0-3), liblz4-1 (= 1.8.3-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.35-4), libmagic1 (= 1:5.35-4), libmount1 (= 2.33.1-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-3), libncurses6 (= 6.1+20181013-2), libncursesw6 (= 6.1+20181013-2), libnettle6 (= 3.4.1-1), libnghttp2-14 (= 1.37.0-1), libp11-kit0 (= 0.23.15-2), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre3 (= 2:8.39-12), libperl5.28 (= 5.28.1-5), libpipeline1 (= 1.5.1-2), libprocps7 (= 2:3.3.15-2), libpsl5 (= 0.20.2-2), libquadmath0 (= 8.3.0-3), librhash0 (= 1.3.8-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2), libsasl2-2 (= 2.1.27+dfsg-1), libsasl2-modules-db (= 2.1.27+dfsg-1), libseccomp2 (= 2.3.3-4), libselinux1 (= 2.8-1+b1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.33.1-0.1), libsmithwaterman-dev (= 0.0+git20160702.2610e25-7), libsmithwaterman0 (= 0.0+git20160702.2610e25-7), libssh2-1 (= 1.8.0-2), libssl1.1 (= 1.1.1b-1), libstdc++-8-dev (= 8.3.0-3), libstdc++6 (= 8.3.0-3), libsuperlu-dev (= 5.2.1+dfsg1-4), libsuperlu5 (= 5.2.1+dfsg1-4), libsystemd0 (= 241-2), libsz2 (= 1.0.2-1), libtasn1-6 (= 4.13-3), libtinfo6 (= 6.1+20181013-2), libtool (= 2.4.6-10), libtsan0 (= 8.3.0-3), libubsan1 (= 8.3.0-3), libuchardet0 (= 0.0.6-3), libudev1 (= 241-2), libunistring2 (= 0.9.10-1), libuuid1 (= 2.33.1-0.1), libuv1 (= 1.24.1-1), libxml2 (= 2.9.4+dfsg1-7+b3), libzstd1 (= 1.3.8+dfsg-3), linux-libc-dev (= 4.19.28-2), login (= 1:4.5-1.1), lsb-base (= 10.2019031300), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.5-2), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20181013-2), ncurses-bin (= 6.1+20181013-2), patch (= 2.7.6-3), perl (= 5.28.1-5), perl-base (= 5.28.1-5), perl-modules-5.28 (= 5.28.1-5), po-debconf (= 1.0.21), procps (= 2:3.3.15-2), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.93-8), tar (= 1.30+dfsg-5), util-linux (= 2.33.1-0.1), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-1), zlib1g-dev (= 1:1.2.11.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="POSIX" SOURCE_DATE_EPOCH="1544684827" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_mipsel.deb ------------------------------------------------------ new Debian package, version 2.0. size 12737224 bytes: control archive=660 bytes. 489 bytes, 12 lines control 318 bytes, 3 lines md5sums Package: tvc-dbgsym Source: tvc Version: 5.0.3+git20151221.80e144e+dfsg-2 Auto-Built-Package: debug-symbols Architecture: mipsel Maintainer: Debian Med Packaging Team Installed-Size: 12791 Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-2) Section: debug Priority: optional Description: debug symbols for tvc Build-Ids: 0bf2ac50600ccccfe07408275dc1f2ac6714d105 32b0f18cba636586fc331328dd8569cb69d3ac4a 8dbf23e781b04face53c7c952952e0a64d66151c drwxr-xr-x root/root 0 2018-12-13 07:07 ./ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/0b/ -rw-r--r-- root/root 9189288 2018-12-13 07:07 ./usr/lib/debug/.build-id/0b/f2ac50600ccccfe07408275dc1f2ac6714d105.debug drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/32/ -rw-r--r-- root/root 1071680 2018-12-13 07:07 ./usr/lib/debug/.build-id/32/b0f18cba636586fc331328dd8569cb69d3ac4a.debug drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/8d/ -rw-r--r-- root/root 2823532 2018-12-13 07:07 ./usr/lib/debug/.build-id/8d/bf23e781b04face53c7c952952e0a64d66151c.debug drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/doc/ lrwxrwxrwx root/root 0 2018-12-13 07:07 ./usr/share/doc/tvc-dbgsym -> tvc tvc_5.0.3+git20151221.80e144e+dfsg-2_mipsel.deb ----------------------------------------------- new Debian package, version 2.0. size 1001680 bytes: control archive=1704 bytes. 1032 bytes, 16 lines control 2459 bytes, 28 lines md5sums Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-2 Architecture: mipsel Maintainer: Debian Med Packaging Team Installed-Size: 3491 Depends: libarmadillo9 (>= 1:9.200.7+dfsg), libbamtools2.5.1, libblas3 | libblas.so.3, libc6 (>= 2.27), libdisorder0 (>= 0.0.2), libgcc1 (>= 1:3.0), libjsoncpp1 (>= 1.7.4), liblapack3 | liblapack.so.3, libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), python Section: science Priority: optional Homepage: http://ioncommunity.thermofisher.com Description: genetic variant caller for Ion Torrent sequencing platforms Torrent Variant Caller (TVC) is a genetic variant caller for Ion Torrent sequencing platforms, and is specially optimized to exploit the underlying flow signal information in the statistical model to evaluate variants. Torrent Variant Caller is designed to call single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), insertions, deletions, and block substitutions. drwxr-xr-x root/root 0 2018-12-13 07:07 ./ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/bin/ -rwxr-xr-x root/root 1226676 2018-12-13 07:07 ./usr/bin/tvc -rwxr-xr-x root/root 226124 2018-12-13 07:07 ./usr/bin/tvcassembly -rwxr-xr-x root/root 673216 2018-12-13 07:07 ./usr/bin/tvcutils -rwxr-xr-x root/root 12989 2015-12-21 20:38 ./usr/bin/variant_caller_pipeline.py drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/examples/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/examples/example1/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/examples/example1/expected/ -rw-r--r-- root/root 6876 2015-12-21 20:38 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drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/pluginMedia/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/pluginMedia/parameter_sets/ -rw-r--r-- root/root 2809 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -rw-r--r-- root/root 2926 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -rw-r--r-- root/root 2826 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -rw-r--r-- root/root 2918 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -rw-r--r-- root/root 3062 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -rw-r--r-- root/root 2628 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -rw-r--r-- root/root 2757 2015-12-21 20:38 ./usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/TVC/sse/ -rw-r--r-- root/root 683778 2015-12-21 20:38 ./usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -rw-r--r-- root/root 451754 2015-12-21 20:38 ./usr/share/TVC/sse/motifset.txt drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/doc/tvc/ -rw-r--r-- root/root 1078 2018-12-13 07:07 ./usr/share/doc/tvc/README.Debian -rw-r--r-- root/root 1047 2018-12-13 07:07 ./usr/share/doc/tvc/changelog.Debian.gz -rw-r--r-- root/root 2939 2018-12-13 07:07 ./usr/share/doc/tvc/copyright drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/lintian/ drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 135 2018-12-13 07:07 ./usr/share/lintian/overrides/tvc +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 153612 Build-Time: 265 Distribution: unstable Foreign Architectures: mipsel Host Architecture: mipsel Install-Time: 26 Job: tvc_5.0.3+git20151221.80e144e+dfsg-2 Lintian: pass Machine Architecture: amd64 Package: tvc Package-Time: 301 Source-Version: 5.0.3+git20151221.80e144e+dfsg-2 Space: 153612 Status: successful Version: 5.0.3+git20151221.80e144e+dfsg-2 -------------------------------------------------------------------------------- Finished at 2019-03-18T10:10:13Z Build needed 00:05:01, 153612k disk space