sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +=================================================================================+ | tvc 5.0.3+git20151221.80e144e+dfsg-2 (mips64el) Fri, 07 Jun 2019 02:14:31 +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: mips64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-51a195ef-c954-49cd-a185-053e5b3a8278' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [210 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 2019-06-06-0813.50.pdiff [1579 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-06-06-1410.53.pdiff [2262 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-06-06-2122.13.pdiff [1643 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-06-06-2122.13.pdiff [1643 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-06-0813.50.pdiff [936 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-06-1410.53.pdiff [2838 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-06-2122.13.pdiff [723 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-06-2122.13.pdiff [723 B] Get:10 http://debian.oregonstate.edu/debian unstable/main mips64el Packages [8014 kB] Fetched 8289 kB in 2s (4256 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 1s (1355 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/tvc-EAuaKY/tvc-5.0.3+git20151221.80e144e+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-EAuaKY' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Fmj2va/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-Fmj2va/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Fmj2va/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-Fmj2va/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Fmj2va/apt_archive ./ Sources [364 B] Get:5 copy:/<>/resolver-Fmj2va/apt_archive ./ Packages [453 B] Fetched 1774 B in 0s (94.3 kB/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-mips64el-linux-gnuabi64 cpp-8-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el dpkg-cross file g++-8-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-8-cross-base gcc-8-mips64el-linux-gnuabi64 gcc-8-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 libatomic1-mips64el-cross libc6-dev-mips64el-cross libc6-mips64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mips64el-cross libgcc1-mips64el-cross libgomp1-mips64el-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mips64el-cross libstdc++6-mips64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mips64el-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch g++-8-multilib-mips64el-linux-gnuabi64 gcc-8-doc libstdc++6-8-dbg-mips64el-cross gcc-8-multilib-mips64el-linux-gnuabi64 libgcc1-dbg-mips64el-cross libgomp1-dbg-mips64el-cross libitm1-dbg-mips64el-cross libatomic1-dbg-mips64el-cross libasan5-dbg-mips64el-cross liblsan0-dbg-mips64el-cross libtsan0-dbg-mips64el-cross libubsan1-dbg-mips64el-cross libmpx2-dbg-mips64el-cross libquadmath0-dbg-mips64el-cross manpages-dev autoconf automake libtool flex bison gdb-mips64el-linux-gnuabi64 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-mips64el-linux-gnuabi64 cpp-8-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el dpkg-cross file g++-8-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-8-cross-base gcc-8-mips64el-linux-gnuabi64 gcc-8-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 libatomic1-mips64el-cross libc6-dev-mips64el-cross libc6-mips64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mips64el-cross libgcc1-mips64el-cross libgomp1-mips64el-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mips64el-cross libstdc++6-mips64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mips64el-cross sbuild-build-depends-core-dummy:mips64el sensible-utils ucf 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 40.4 MB of archives. After this operation, 151 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Fmj2va/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [876 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-mips64el-linux-gnuabi64 amd64 2.31.1-16 [2489 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mips64el-linux-gnuabi64-base amd64 8.3.0-7cross1 [191 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6277 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-7cross1 [186 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-mips64el-cross all 2.28-10cross2 [1355 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-mips64el-cross all 1:8.3.0-7cross1 [68.8 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-mips64el-cross all 8.3.0-7cross1 [66.0 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-mips64el-cross all 8.3.0-7cross1 [7384 B] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-mips64el-cross all 8.3.0-7cross1 [235 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6691 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [1472 B] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-mips64el-cross all 8.3.0-7cross1 [310 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-mips64el-cross all 4.19.28-2cross2 [1240 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-mips64el-cross all 2.28-10cross2 [2512 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-mips64el-cross all 8.3.0-7cross1 [1559 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6850 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 g++-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [1192 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 2.6.15-3 [38.7 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-mips64el all 12.6 [6584 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.4 MB in 1s (66.0 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11954 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) ... 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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 (8.3.0-7cross1) ... Setting up libmagic1:amd64 (1:5.35-4) ... Setting up libc6-mips64el-cross (2.28-10cross2) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up file (1:5.35-4) ... Setting up libyaml-perl (1.27-1) ... Setting up binutils-mips64el-linux-gnuabi64 (2.31.1-16) ... 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 (2.6.15-3) ... Setting up gcc-8-mips64el-linux-gnuabi64-base:amd64 (8.3.0-7cross1) ... Setting up sensible-utils (0.0.12) ... Setting up linux-libc-dev-mips64el-cross (4.19.28-2cross2) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libgomp1-mips64el-cross (8.3.0-7cross1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up cpp-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up libatomic1-mips64el-cross (8.3.0-7cross1) ... Setting up libgcc1-mips64el-cross (1:8.3.0-7cross1) ... Setting up libc6-dev-mips64el-cross (2.28-10cross2) ... Setting up ucf (3.0038+nmu1) ... Setting up libstdc++6-mips64el-cross (8.3.0-7cross1) ... Setting up cpp-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up libgcc-8-dev-mips64el-cross (8.3.0-7cross1) ... 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 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 libstdc++-8-dev-mips64el-cross (8.3.0-7cross1) ... Setting up gcc-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up g++-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up g++-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-mips64el (12.6) ... Setting up sbuild-build-depends-core-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (mips64el included in any) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-Fmj2va/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-Fmj2va/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Fmj2va/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Fmj2va/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Fmj2va/apt_archive ./ Sources [484 B] Get:5 copy:/<>/resolver-Fmj2va/apt_archive ./ Packages [571 B] Fetched 2018 B in 0s (114 kB/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:mips64el 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 844 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Fmj2va/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [844 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 844 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:mips64el. (Reading database ... 15129 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_mips64el.deb ... Unpacking sbuild-build-depends-essential-dummy:mips64el (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:mips64el (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-Fmj2va/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-Fmj2va/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Fmj2va/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Fmj2va/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Fmj2va/apt_archive ./ Sources [678 B] Get:5 copy:/<>/resolver-Fmj2va/apt_archive ./ Packages [761 B] Fetched 2402 B in 0s (127 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:mips64el gettext gettext-base groff-base hdf5-helpers:mips64el intltool-debian libaec-dev:mips64el libaec0:mips64el libarchive-zip-perl libarchive13 libarmadillo-dev:mips64el libarmadillo9:mips64el libarpack2:mips64el libarpack2-dev:mips64el libatomic1:mips64el libbamtools-dev:mips64el libbamtools2.5.1:mips64el libblas-dev:mips64el libblas3:mips64el libboost-math-dev:mips64el libboost-math1.67-dev:mips64el libboost-math1.67.0:mips64el libboost1.67-dev:mips64el libbsd0 libc6:mips64el libc6-dev:mips64el libcroco3 libcurl4 libdisorder-dev:mips64el libdisorder0:mips64el libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-8-dev:mips64el libgcc1:mips64el libgfortran5:mips64el libglib2.0-0 libgomp1:mips64el libgssapi-krb5-2 libhdf5-103:mips64el libhdf5-cpp-103:mips64el libhdf5-dev:mips64el libjpeg62-turbo:mips64el libjpeg62-turbo-dev:mips64el libjsoncpp-dev:mips64el libjsoncpp1 libjsoncpp1:mips64el libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:mips64el liblapack3:mips64el libldap-2.4-2 libldap-common libncurses6 libnghttp2-14 libpipeline1 libprocps7 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:mips64el libsmithwaterman0:mips64el libssh2-1 libssl1.1 libstdc++-8-dev:mips64el libstdc++6:mips64el libsuperlu-dev:mips64el libsuperlu5:mips64el libsz2:mips64el libtool libuchardet0 libuv1 linux-libc-dev:mips64el lsb-base m4 man-db po-debconf procps zlib1g:mips64el zlib1g-dev:mips64el 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:mips64el libbamtools-doc:mips64el liblapack-doc:mips64el libboost1.67-doc:mips64el libboost-atomic1.67-dev:mips64el libboost-chrono1.67-dev:mips64el libboost-container1.67-dev:mips64el libboost-date-time1.67-dev:mips64el libboost-exception1.67-dev:mips64el libboost-filesystem1.67-dev:mips64el libboost-graph1.67-dev:mips64el libboost-graph-parallel1.67-dev:mips64el libboost-iostreams1.67-dev:mips64el libboost-locale1.67-dev:mips64el libboost-log1.67-dev:mips64el libboost-mpi1.67-dev:mips64el libboost-mpi-python1.67-dev:mips64el libboost-numpy1.67-dev:mips64el libboost-program-options1.67-dev:mips64el libboost-python1.67-dev:mips64el libboost-random1.67-dev:mips64el libboost-regex1.67-dev:mips64el libboost-serialization1.67-dev:mips64el libboost-signals1.67-dev:mips64el libboost-stacktrace1.67-dev:mips64el libboost-system1.67-dev:mips64el libboost-test1.67-dev:mips64el libboost-thread1.67-dev:mips64el libboost-timer1.67-dev:mips64el libboost-type-erasure1.67-dev:mips64el libboost-wave1.67-dev:mips64el libboost1.67-tools-dev:mips64el libmpfrc++-dev:mips64el libntl-dev:mips64el glibc-doc:mips64el libc-l10n:mips64el locales:mips64el manpages-dev:mips64el krb5-doc krb5-user libhdf5-doc:mips64el libstdc++-8-doc:mips64el libsuperlu-doc:mips64el libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:mips64el 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:mips64el gettext gettext-base groff-base hdf5-helpers:mips64el intltool-debian libaec-dev:mips64el libaec0:mips64el libarchive-zip-perl libarchive13 libarmadillo-dev:mips64el libarmadillo9:mips64el libarpack2:mips64el libarpack2-dev:mips64el libatomic1:mips64el libbamtools-dev:mips64el libbamtools2.5.1:mips64el libblas-dev:mips64el libblas3:mips64el libboost-math-dev:mips64el libboost-math1.67-dev:mips64el libboost-math1.67.0:mips64el libboost1.67-dev:mips64el libbsd0 libc6:mips64el libc6-dev:mips64el libcroco3 libcurl4 libdisorder-dev:mips64el libdisorder0:mips64el libelf1 libexpat1 libfile-stripnondeterminism-perl libgcc-8-dev:mips64el libgcc1:mips64el libgfortran5:mips64el libglib2.0-0 libgomp1:mips64el libgssapi-krb5-2 libhdf5-103:mips64el libhdf5-cpp-103:mips64el libhdf5-dev:mips64el libjpeg62-turbo:mips64el libjpeg62-turbo-dev:mips64el libjsoncpp-dev:mips64el libjsoncpp1 libjsoncpp1:mips64el libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:mips64el liblapack3:mips64el libldap-2.4-2 libldap-common libncurses6 libnghttp2-14 libpipeline1 libprocps7 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:mips64el libsmithwaterman0:mips64el libssh2-1 libssl1.1 libstdc++-8-dev:mips64el libstdc++6:mips64el libsuperlu-dev:mips64el libsuperlu5:mips64el libsz2:mips64el libtool libuchardet0 libuv1 linux-libc-dev:mips64el lsb-base m4 man-db po-debconf procps sbuild-build-depends-tvc-dummy:mips64el zlib1g:mips64el zlib1g-dev:mips64el 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 47.2 MB of archives. After this operation, 336 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Fmj2va/apt_archive ./ sbuild-build-depends-tvc-dummy 0.invalid.0 [924 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 10.2019051400 [28.4 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 1.1.1c-1 [1535 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 1.8.0-2.1 [140 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libcurl4 amd64 7.64.0-3 [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 0.176-1.1 [161 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 2.58.3-2 [1259 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 mips64el gcc-8-base mips64el 8.3.0-7 [191 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main mips64el hdf5-helpers mips64el 1.10.4+repack-10 [35.2 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc1 mips64el 1:8.3.0-7 [68.5 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main mips64el libc6 mips64el 2.28-10 [2562 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main mips64el libaec0 mips64el 1.0.2-1 [20.3 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main mips64el libsz2 mips64el 1.0.2-1 [6736 B] Get:60 http://debian.oregonstate.edu/debian unstable/main mips64el libaec-dev mips64el 1.0.2-1 [19.6 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main mips64el zlib1g mips64el 1:1.2.11.dfsg-1 [91.1 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main mips64el libgfortran5 mips64el 8.3.0-7 [272 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main mips64el libblas3 mips64el 3.8.0-2 [110 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main mips64el liblapack3 mips64el 3.8.0-2 [1557 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main mips64el libarpack2 mips64el 3.7.0-2 [85.3 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++6 mips64el 8.3.0-7 [348 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main mips64el libsuperlu5 mips64el 5.2.1+dfsg1-4 [125 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main mips64el libarmadillo9 mips64el 1:9.200.7+dfsg-1 [89.9 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main mips64el libblas-dev mips64el 3.8.0-2 [125 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main mips64el liblapack-dev mips64el 3.8.0-2 [1787 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main mips64el libarpack2-dev mips64el 3.7.0-2 [112 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main mips64el libhdf5-103 mips64el 1.10.4+repack-10 [927 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main mips64el linux-libc-dev mips64el 4.19.37-3 [1178 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main mips64el libc6-dev mips64el 2.28-10 [2513 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main mips64el zlib1g-dev mips64el 1:1.2.11.dfsg-1 [215 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main mips64el libjpeg62-turbo mips64el 1:1.5.2-2+b1 [139 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main mips64el libjpeg62-turbo-dev mips64el 1:1.5.2-2+b1 [218 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main mips64el libhdf5-cpp-103 mips64el 1.10.4+repack-10 [115 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main mips64el libhdf5-dev mips64el 1.10.4+repack-10 [2595 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main mips64el libsuperlu-dev mips64el 5.2.1+dfsg1-4 [18.4 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main mips64el libarmadillo-dev mips64el 1:9.200.7+dfsg-1 [360 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main mips64el libatomic1 mips64el 8.3.0-7 [7432 B] Get:83 http://debian.oregonstate.edu/debian unstable/main mips64el libbamtools2.5.1 mips64el 2.5.1+dfsg-3 [139 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main mips64el libbamtools-dev mips64el 2.5.1+dfsg-3 [21.9 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main mips64el libgomp1 mips64el 8.3.0-7 [67.3 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc-8-dev mips64el 8.3.0-7 [234 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++-8-dev mips64el 8.3.0-7 [1573 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main mips64el libboost1.67-dev mips64el 1.67.0-13 [8386 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main mips64el libboost-math1.67.0 mips64el 1.67.0-13 [518 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main mips64el libboost-math1.67-dev mips64el 1.67.0-13 [1076 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main mips64el libboost-math-dev mips64el 1.67.0.1 [3852 B] Get:92 http://debian.oregonstate.edu/debian unstable/main mips64el libdisorder0 mips64el 0.0.2+git20130809.8062ee1-1 [4288 B] Get:93 http://debian.oregonstate.edu/debian unstable/main mips64el libdisorder-dev mips64el 0.0.2+git20130809.8062ee1-1 [4324 B] Get:94 http://debian.oregonstate.edu/debian unstable/main mips64el libjsoncpp1 mips64el 1.7.4-3 [72.1 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main mips64el libjsoncpp-dev mips64el 1.7.4-3 [99.9 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main mips64el libsmithwaterman0 mips64el 0.0+git20160702.2610e25-7 [33.1 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main mips64el libsmithwaterman-dev mips64el 0.0+git20160702.2610e25-7 [41.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.2 MB in 1s (59.6 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15129 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 libexpat1:amd64 (2.2.6-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up lsb-base (10.2019051400) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up hdf5-helpers:mips64el (1.10.4+repack-10) ... Setting up libarchive13:amd64 (3.3.3-4) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1c-1) ... Setting up libprocps7:amd64 (2:3.3.15-2) ... Setting up libnghttp2-14:amd64 (1.37.0-1) ... Setting up linux-libc-dev:mips64el (4.19.37-3) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libldap-common (2.4.47+dfsg-3) ... Setting up libkrb5support0:amd64 (1.17-2) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:amd64 (1.24.1-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up gcc-8-base:mips64el (8.3.0-7) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libk5crypto3:amd64 (1.17-2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1) ... 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 (1.8.0-2.1) ... 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 (0.176-1.1) ... 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 (7.64.0-3) ... 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:mips64el (2.28-10) ... Setting up libc6-dev:mips64el (2.28-10) ... Setting up libdisorder0:mips64el (0.0.2+git20130809.8062ee1-1) ... Setting up libgcc1:mips64el (1:8.3.0-7) ... Setting up debhelper (12.1.1) ... Setting up zlib1g:mips64el (1:1.2.11.dfsg-1) ... Setting up libgomp1:mips64el (8.3.0-7) ... Setting up libaec0:mips64el (1.0.2-1) ... Setting up libjpeg62-turbo:mips64el (1:1.5.2-2+b1) ... Setting up libjpeg62-turbo-dev:mips64el (1:1.5.2-2+b1) ... Setting up libatomic1:mips64el (8.3.0-7) ... Setting up libdisorder-dev:mips64el (0.0.2+git20130809.8062ee1-1) ... Setting up libgcc-8-dev:mips64el (8.3.0-7) ... Setting up libgfortran5:mips64el (8.3.0-7) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up zlib1g-dev:mips64el (1:1.2.11.dfsg-1) ... Setting up libstdc++6:mips64el (8.3.0-7) ... Setting up libsz2:mips64el (1.0.2-1) ... Setting up libjsoncpp1:mips64el (1.7.4-3) ... Setting up libstdc++-8-dev:mips64el (8.3.0-7) ... Setting up libboost1.67-dev:mips64el (1.67.0-13) ... Setting up libjsoncpp-dev:mips64el (1.7.4-3) ... Setting up libaec-dev:mips64el (1.0.2-1) ... Setting up libsmithwaterman0:mips64el (0.0+git20160702.2610e25-7) ... Setting up libboost-math1.67.0:mips64el (1.67.0-13) ... Setting up libblas3:mips64el (3.8.0-2) ... update-alternatives: using /usr/lib/mips64el-linux-gnuabi64/blas/libblas.so.3 to provide /usr/lib/mips64el-linux-gnuabi64/libblas.so.3 (libblas.so.3-mips64el-linux-gnuabi64) in auto mode Setting up libhdf5-103:mips64el (1.10.4+repack-10) ... Setting up libbamtools2.5.1:mips64el (2.5.1+dfsg-3) ... Setting up libsmithwaterman-dev:mips64el (0.0+git20160702.2610e25-7) ... Setting up libblas-dev:mips64el (3.8.0-2) ... update-alternatives: using /usr/lib/mips64el-linux-gnuabi64/blas/libblas.so to provide /usr/lib/mips64el-linux-gnuabi64/libblas.so (libblas.so-mips64el-linux-gnuabi64) in auto mode Setting up liblapack3:mips64el (3.8.0-2) ... update-alternatives: using /usr/lib/mips64el-linux-gnuabi64/lapack/liblapack.so.3 to provide /usr/lib/mips64el-linux-gnuabi64/liblapack.so.3 (liblapack.so.3-mips64el-linux-gnuabi64) in auto mode Setting up libboost-math1.67-dev:mips64el (1.67.0-13) ... Setting up libboost-math-dev:mips64el (1.67.0.1) ... Setting up libhdf5-cpp-103:mips64el (1.10.4+repack-10) ... Setting up libarpack2:mips64el (3.7.0-2) ... Setting up libsuperlu5:mips64el (5.2.1+dfsg1-4) ... Setting up libbamtools-dev:mips64el (2.5.1+dfsg-3) ... Setting up libhdf5-dev:mips64el (1.10.4+repack-10) ... update-alternatives: using /usr/lib/mips64el-linux-gnuabi64/pkgconfig/hdf5-serial.pc to provide /usr/lib/mips64el-linux-gnuabi64/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up liblapack-dev:mips64el (3.8.0-2) ... update-alternatives: using /usr/lib/mips64el-linux-gnuabi64/lapack/liblapack.so to provide /usr/lib/mips64el-linux-gnuabi64/liblapack.so (liblapack.so-mips64el-linux-gnuabi64) in auto mode Setting up libarmadillo9:mips64el (1:9.200.7+dfsg-1) ... Setting up libsuperlu-dev:mips64el (5.2.1+dfsg1-4) ... Setting up libarpack2-dev:mips64el (3.7.0-2) ... Setting up libarmadillo-dev:mips64el (1:9.200.7+dfsg-1) ... Setting up sbuild-build-depends-tvc-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.7 g++-8_8.3.0-7 gcc-8_8.3.0-7 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-mips64el-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-mips64el-cross_8.3.0-7cross1 linux-libc-dev_4.19.37-3 Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16 binutils-common_2.31.1-16 binutils-mips64el-linux-gnuabi64_2.31.1-16 binutils-x86-64-linux-gnu_2.31.1-16 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_8.3.0-7 cpp-8-mips64el-linux-gnuabi64_8.3.0-7cross1 cpp-mips64el-linux-gnuabi64_4:8.3.0-1 cross-config_2.6.15-3 crossbuild-essential-mips64el_12.6 dash_0.5.10.2-5 debconf_1.5.72 debhelper_12.1.1 debian-archive-keyring_2019.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.45.1-3 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_8.3.0-7 g++-8-mips64el-linux-gnuabi64_8.3.0-7cross1 g++-mips64el-linux-gnuabi64_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-7 gcc-8-base_8.3.0-7 gcc-8-cross-base_8.3.0-7cross1 gcc-8-mips64el-linux-gnuabi64_8.3.0-7cross1 gcc-8-mips64el-linux-gnuabi64-base_8.3.0-7cross1 gcc-mips64el-linux-gnuabi64_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.13-2 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_1.8.2 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_3.7.0-2 libarpack2-dev_3.7.0-2 libasan5_8.3.0-7 libatomic1_8.3.0-7 libatomic1-mips64el-cross_8.3.0-7cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.31.1-16 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_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-dev_2.28-10 libc6-dev-mips64el-cross_2.28-10cross2 libc6-mips64el-cross_2.28-10cross2 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-7 libcom-err2_1.45.1-3 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libcurl4_7.64.0-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-3 libdisorder-dev_0.0.2+git20130809.8062ee1-1 libdisorder0_0.0.2+git20130809.8062ee1-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.6-1 libext2fs2_1.45.1-3 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_8.3.0-7 libgcc-8-dev-mips64el-cross_8.3.0-7cross1 libgcc1_1:8.3.0-7 libgcc1-mips64el-cross_1:8.3.0-7cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libgfortran5_8.3.0-7 libglib2.0-0_2.58.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-3 libgomp1_8.3.0-7 libgomp1-mips64el-cross_8.3.0-7cross1 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_8.3.0-7 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_8.3.0-7 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_8.3.0-7 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_5.28.1-6 libpipeline1_1.5.1-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libquadmath0_8.3.0-7 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_1.45.1-3 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-mips64el-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-mips64el-cross_8.3.0-7cross1 libsuperlu-dev_5.2.1+dfsg1-4 libsuperlu5_5.2.1+dfsg1-4 libsystemd0_241-5 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-7 libubsan1_8.3.0-7 libuchardet0_0.0.6-3 libudev1_241-5 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_4.19.37-3 linux-libc-dev-mips64el-cross_4.19.28-2cross2 login_1:4.5-1.1 lsb-base_10.2019051400 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_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 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-6 tzdata_2019a-1 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.mips64el 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-51a195ef-c954-49cd-a185-053e5b3a8278 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 mips64el-linux-gnuabi64 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 mips64el 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-mips64el-linux-gnuabi64 && 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=mips64el -DCMAKE_C_COMPILER=mips64el-linux-gnuabi64-gcc -DCMAKE_CXX_COMPILER=mips64el-linux-gnuabi64-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/mips64el-linux-gnuabi64-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/mips64el-linux-gnuabi64-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/mips64el-linux-gnuabi64-qmake -DCMAKE_INSTALL_LIBDIR=lib/mips64el-linux-gnuabi64 .. -- 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/mips64el-linux-gnuabi64-gcc -- Check for working C compiler: /usr/bin/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-g++ -- Check for working CXX compiler: /usr/bin/mips64el-linux-gnuabi64-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-mips64el-linux-gnuabi64 dh_auto_build -a cd obj-mips64el-linux-gnuabi64 && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc make[1]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' /usr/bin/cmake -S/<>/tvc-5.0.3+git20151221.80e144e+dfsg -B/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 && /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-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= Scanning dependencies of target tvcassembly make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' [ 1%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o /usr/bin/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-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-mips64el-linux-gnuabi64/IonVersion.cpp [ 10%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/mips64el-linux-gnuabi64-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-mips64el-linux-gnuabi64' [ 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-mips64el-linux-gnuabi64' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 && /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-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles/tvc.dir/DependInfo.cmake --color= Scanning dependencies of target tvc make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' [ 12%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o /usr/bin/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-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/OrderedBAMWriter.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/OrderedBAMWriter.cpp [ 17%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o /usr/bin/mips64el-linux-gnuabi64-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/SampleManager.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp [ 18%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/mips64el-linux-gnuabi64-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/mips64el-linux-gnuabi64-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/HandleVariant.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp [ 21%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o /usr/bin/mips64el-linux-gnuabi64-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/HotspotReader.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HotspotReader.cpp [ 23%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/mips64el-linux-gnuabi64-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/MetricsManager.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp [ 25%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o /usr/bin/mips64el-linux-gnuabi64-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 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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/external/vcflib/split.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 59%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/mips64el-linux-gnuabi64-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/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/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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o /usr/bin/mips64el-linux-gnuabi64-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 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-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/VariantCaller/TargetsManager.cpp.o -c /<>/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp [ 89%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o /usr/bin/mips64el-linux-gnuabi64-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/external/vcflib/Variant.cpp [ 92%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o /usr/bin/mips64el-linux-gnuabi64-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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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-mips64el-linux-gnuabi64' [100%] Built target tvcutils make[2]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' /usr/bin/cmake -E cmake_progress_start /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles 0 make[1]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' 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-mips64el-linux-gnuabi64 && 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-mips64el-linux-gnuabi64' /usr/bin/cmake -S/<>/tvc-5.0.3+git20151221.80e144e+dfsg -B/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 && /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-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' [ 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-mips64el-linux-gnuabi64' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 && /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-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' [ 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-mips64el-linux-gnuabi64' cd /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 && /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-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64 /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' [100%] Built target tvcutils make[2]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' /usr/bin/cmake -E cmake_progress_start /<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/tvc-5.0.3+git20151221.80e144e+dfsg/obj-mips64el-linux-gnuabi64' 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-mips64el-linux-gnuabi64' 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 libblas.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 liblapack.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_mips64el.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_mips64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../tvc_5.0.3+git20151221.80e144e+dfsg-2_mips64el.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 2019-06-07T02:19:35Z 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-Fmj2va/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-Fmj2va/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Fmj2va/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Fmj2va/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Fmj2va/apt_archive ./ Sources [801 B] Get:5 copy:/<>/resolver-Fmj2va/apt_archive ./ Packages [874 B] Fetched 2638 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:mips64el t1utils 0 upgraded, 47 newly installed, 0 to remove and 0 not upgraded. Need to get 6238 kB of archives. After this operation, 16.6 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Fmj2va/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 2.2.13-2 [512 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.27.2-2 [640 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.13-2 [866 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 2.15.0 [1181 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6238 kB in 0s (41.7 MB/s) Selecting previously unselected package netbase. (Reading database ... 36134 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_2.2.13-2_amd64.deb ... Unpacking gpgconf (2.2.13-2) ... Selecting previously unselected package libsqlite3-0:amd64. 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Preparing to unpack .../29-libipc-system-simple-perl_1.25-4_all.deb ... Unpacking libipc-system-simple-perl (1.25-4) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../30-libfile-basedir-perl_0.08-1_all.deb ... Unpacking libfile-basedir-perl (0.08-1) ... Selecting previously unselected package libfuture-perl. Preparing to unpack .../31-libfuture-perl_0.39-1_all.deb ... Unpacking libfuture-perl (0.39-1) ... Selecting previously unselected package libstruct-dumb-perl. Preparing to unpack .../32-libstruct-dumb-perl_0.09-1_all.deb ... Unpacking libstruct-dumb-perl (0.09-1) ... Selecting previously unselected package libio-async-perl. Preparing to unpack .../33-libio-async-perl_0.72-1_all.deb ... Unpacking libio-async-perl (0.72-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../34-libio-pty-perl_1%3a1.08-1.1+b5_amd64.deb ... Unpacking libio-pty-perl (1:1.08-1.1+b5) ... 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Preparing to unpack .../46-sbuild-build-depends-lintian-dummy_0.invalid.0_mips64el.deb ... Unpacking sbuild-build-depends-lintian-dummy:mips64el (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.34+b1) ... Setting up libstruct-dumb-perl (0.09-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libclone-perl (0.41-1+b1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libsqlite3-0:amd64 (3.27.2-2) ... Setting up libfuture-perl (0.39-1) ... Setting up libyaml-libyaml-perl (0.76+repack-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libtext-levenshtein-perl (0.13-1) ... Setting up libassuan0:amd64 (2.5.2-1) ... Setting up libio-async-perl (0.72-1) ... Setting up patchutils (0.3.4-2) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.25-4) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up t1utils (1.41-3) ... Setting up diffstat (1.62-1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsub-name-perl (0.21-1+b3) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up netbase (5.6) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (7.0-5) ... Setting up liburi-perl (1.76-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libnet-ssleay-perl (1.85-2+b1) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b4) ... Setting up libnet-dns-perl (1.19-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.13-2) ... Setting up libio-socket-ssl-perl (2.060-3) ... Setting up gpg (2.2.13-2) ... Setting up libcgi-pm-perl (4.40-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmailtools-perl (2.18-1) ... Setting up libparse-debianchangelog-perl (1.2.0-13) ... Setting up libemail-valid-perl (1.202-1) ... Setting up lintian (2.15.0) ... Setting up sbuild-build-depends-lintian-dummy:mips64el (0.invalid.0) ... Processing triggers for man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.28-10) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ tvc_5.0.3+git20151221.80e144e+dfsg-2_mips64el.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: mips64el 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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tvc_5.0.3+git20151221.80e144e+dfsg-2_mips64el.buildinfo 7baeeec5539bb2ed9ac0dd1105dd18f0 1005108 science optional tvc_5.0.3+git20151221.80e144e+dfsg-2_mips64el.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: tvc Binary: tvc Architecture: mips64el Version: 5.0.3+git20151221.80e144e+dfsg-2 Checksums-Md5: 3b45e626bac7de3084ae0afc914fa0a2 13038224 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_mips64el.deb 7baeeec5539bb2ed9ac0dd1105dd18f0 1005108 tvc_5.0.3+git20151221.80e144e+dfsg-2_mips64el.deb Checksums-Sha1: 955eafa1b6dc6c660b08f4ece14bf48a6ddb1c89 13038224 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_mips64el.deb dac753443586c5ec0d776c4f028a5f20aa89933a 1005108 tvc_5.0.3+git20151221.80e144e+dfsg-2_mips64el.deb Checksums-Sha256: 9fd8c0bbadaf6317e92b8b370faef64d207fa4d5c374807fdbe8042b7a965d70 13038224 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-2_mips64el.deb e3980342648f9aa5b8aaab62bf62f5188fbd8059de8d9947c1db397dab12aec1 1005108 tvc_5.0.3+git20151221.80e144e+dfsg-2_mips64el.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Fri, 07 Jun 2019 02:19:35 +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 (= 10.3), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.31.1-16), binutils-common (= 2.31.1-16), binutils-x86-64-linux-gnu (= 2.31.1-16), 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 (= 8.3.0-7), dash (= 0.5.10.2-5), debconf (= 1.5.72), debhelper (= 12.1.1), debianutils (= 4.8.6.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.1.2-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), 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 (= 8.3.0-7), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-7), gcc-8-base (= 8.3.0-7), 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 (= 3.7.0-2), libarpack2-dev (= 3.7.0-2), libasan5 (= 8.3.0-7), libatomic1 (= 8.3.0-7), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.4-3), libaudit1 (= 1:2.8.4-3), libbamtools-dev (= 2.5.1+dfsg-3), libbamtools2.5.1 (= 2.5.1+dfsg-3), libbinutils (= 2.31.1-16), 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 (= 2.28-10), libc-dev-bin (= 2.28-10), libc6 (= 2.28-10), libc6-dev (= 2.28-10), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 8.3.0-7), libcom-err2 (= 1.45.1-3), libcroco3 (= 0.6.12-3), libcurl4 (= 7.64.0-3), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.249), libdisorder-dev (= 0.0.2+git20130809.8062ee1-1), libdisorder0 (= 0.0.2+git20130809.8062ee1-1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), 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 (= 8.3.0-7), libgcc1 (= 1:8.3.0-7), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-4), libgdbm6 (= 1.18.1-4), libgfortran5 (= 8.3.0-7), libglib2.0-0 (= 2.58.3-2), libgmp10 (= 2:6.1.2+dfsg-4), libgnutls30 (= 3.6.7-3), libgomp1 (= 8.3.0-7), 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 (= 8.3.0-7), 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 (= 8.3.0-7), 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 (= 8.3.0-7), 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 (= 5.28.1-6), libpipeline1 (= 1.5.1-2), libprocps7 (= 2:3.3.15-2), libpsl5 (= 0.20.2-2), libquadmath0 (= 8.3.0-7), 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 (= 1.8.0-2.1), libssl1.1 (= 1.1.1c-1), libstdc++-8-dev (= 8.3.0-7), libstdc++6 (= 8.3.0-7), libsuperlu-dev (= 5.2.1+dfsg1-4), libsuperlu5 (= 5.2.1+dfsg1-4), libsystemd0 (= 241-5), libsz2 (= 1.0.2-1), libtasn1-6 (= 4.13-3), libtinfo6 (= 6.1+20181013-2), libtool (= 2.4.6-10), libtsan0 (= 8.3.0-7), libubsan1 (= 8.3.0-7), libuchardet0 (= 0.0.6-3), libudev1 (= 241-5), 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 (= 4.19.37-3), login (= 1:4.5-1.1), lsb-base (= 10.2019051400), 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 (= 5.28.1-6), perl-base (= 5.28.1-6), perl-modules-5.28 (= 5.28.1-6), 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-6), 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_mips64el.deb -------------------------------------------------------- new Debian package, version 2.0. size 13038224 bytes: control archive=660 bytes. 491 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: mips64el Maintainer: Debian Med Packaging Team Installed-Size: 15198 Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-2) Section: debug Priority: optional Description: debug symbols for tvc Build-Ids: 205ca7bed77020ea4d98c625f3cfa371e4c2ee9a 28f29476cf41ae873dc716969544556888c9ca92 af0deef403aa750102436ada1811bd44bdf164cb 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/20/ -rw-r--r-- root/root 10640632 2018-12-13 07:07 ./usr/lib/debug/.build-id/20/5ca7bed77020ea4d98c625f3cfa371e4c2ee9a.debug drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/28/ -rw-r--r-- root/root 1311368 2018-12-13 07:07 ./usr/lib/debug/.build-id/28/f29476cf41ae873dc716969544556888c9ca92.debug drwxr-xr-x root/root 0 2018-12-13 07:07 ./usr/lib/debug/.build-id/af/ -rw-r--r-- root/root 3597080 2018-12-13 07:07 ./usr/lib/debug/.build-id/af/0deef403aa750102436ada1811bd44bdf164cb.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_mips64el.deb ------------------------------------------------- new Debian package, version 2.0. size 1005108 bytes: control archive=1700 bytes. 1034 bytes, 16 lines control 2459 bytes, 28 lines md5sums Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-2 Architecture: mips64el Maintainer: Debian Med Packaging Team Installed-Size: 3595 Depends: libarmadillo9 (>= 1:9.200.7+dfsg), libbamtools2.5.1, libblas3 | libblas.so.3, libc6 (>= 2.27), libdisorder0 (>= 0.0.2), libgcc1 (>= 1:4.5), 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 1281296 2018-12-13 07:07 ./usr/bin/tvc -rwxr-xr-x root/root 228936 2018-12-13 07:07 ./usr/bin/tvcassembly -rwxr-xr-x root/root 721408 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 ./usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -rw-r--r-- root/root 6479 2015-12-21 20:38 ./usr/share/TVC/examples/example1/expected/small_variants.vcf -rw-r--r-- root/root 108 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.dict -rw-r--r-- root/root 3400 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta -rw-r--r-- root/root 22 2015-12-21 20:38 ./usr/share/TVC/examples/example1/reference.fasta.fai -rw-r--r-- root/root 225904 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam -rw-r--r-- root/root 96 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bam.bai -rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test.bed -rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_merged_plain.bed -rw-r--r-- root/root 13 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_original.bed -rw-r--r-- root/root 70 2015-12-21 20:38 ./usr/share/TVC/examples/example1/test_unmerged_detail.bed 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: 219432 Build-Time: 262 Distribution: unstable Foreign Architectures: mips64el Host Architecture: mips64el Install-Time: 31 Job: tvc_5.0.3+git20151221.80e144e+dfsg-2 Lintian: pass Machine Architecture: amd64 Package: tvc Package-Time: 304 Source-Version: 5.0.3+git20151221.80e144e+dfsg-2 Space: 219432 Status: successful Version: 5.0.3+git20151221.80e144e+dfsg-2 -------------------------------------------------------------------------------- Finished at 2019-06-07T02:19:35Z Build needed 00:05:04, 219432k disk space