sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | tvc 5.0.3+git20151221.80e144e+dfsg-3 (armel) Mon, 02 Mar 2020 03:35:39 +0000 | +==============================================================================+ Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-3 Source Version: 5.0.3+git20151221.80e144e+dfsg-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-9133500f-fd05-4cc2-b035-763b57e3c708' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-qYwo4Z/resolver-wAUV7Z' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [142 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 2020-03-01-0816.41.pdiff [4967 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-03-01-1417.53.pdiff [11.2 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-03-01-2019.29.pdiff [12.6 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2020-03-02-0215.51.pdiff [9104 B] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2020-03-02-0215.51.pdiff [9104 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-03-01-0816.41.pdiff [4515 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-03-01-1417.53.pdiff [12.2 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-03-01-2019.29.pdiff [16.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-03-02-0215.51.pdiff [9292 B] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-03-02-0215.51.pdiff [9292 B] Get:12 http://debian.oregonstate.edu/debian unstable/main armel Packages [7923 kB] Fetched 8202 kB in 2s (4922 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 756 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (dsc) [2200 B] Get:2 http://debian.oregonstate.edu/debian unstable/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (tar) [745 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (diff) [8968 B] Fetched 756 kB in 0s (14.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/tvc-qYwo4Z/tvc-5.0.3+git20151221.80e144e+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-qYwo4Z' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [445 B] Get:5 copy:/<>/apt_archive ./ Packages [536 B] Fetched 1938 B in 0s (96.6 kB/s) Reading package lists... Reading package lists... Install main 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 binutils-arm-linux-gnueabi bsdmainutils build-essential cmake cmake-data cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base hdf5-helpers:armel intltool-debian libaec-dev:armel libaec0:armel libarchive-zip-perl libarchive13 libarmadillo-dev:armel libarmadillo9:armel libarpack2:armel libarpack2-dev:armel libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbamtools-dev:armel libbamtools2.5.1:armel libblas-dev:armel libblas3:armel libboost-math-dev:armel libboost-math1.67-dev:armel libboost-math1.67.0:armel libboost1.67-dev:armel libbrotli1 libbsd0 libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdisorder-dev:armel libdisorder0:armel libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgfortran5:armel libglib2.0-0 libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2 libhdf5-103:armel libhdf5-cpp-103:armel libhdf5-dev:armel libicu63 libio-string-perl libjpeg62-turbo:armel libjpeg62-turbo-dev:armel libjsoncpp-dev:armel libjsoncpp1 libjsoncpp1:armel libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:armel liblapack3:armel libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:armel libsmithwaterman0:armel libssh2-1 libssl1.1 libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libsuperlu-dev:armel libsuperlu5:armel libsz2:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libuv1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db po-debconf procps sensible-utils ucf zlib1g:armel zlib1g-dev:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation cmake-doc ninja-build gcc-9-locales cpp-doc dh-make binutils-multiarch g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libitpp-dev:armel libbamtools-doc:armel liblapack-doc:armel libboost1.67-doc:armel libboost-atomic1.67-dev:armel libboost-chrono1.67-dev:armel libboost-container1.67-dev:armel libboost-context1.67-dev:armel libboost-contract1.67-dev:armel libboost-coroutine1.67-dev:armel libboost-date-time1.67-dev:armel libboost-exception1.67-dev:armel libboost-fiber1.67-dev:armel libboost-filesystem1.67-dev:armel libboost-graph1.67-dev:armel libboost-graph-parallel1.67-dev:armel libboost-iostreams1.67-dev:armel libboost-locale1.67-dev:armel libboost-log1.67-dev:armel libboost-mpi1.67-dev:armel libboost-mpi-python1.67-dev:armel libboost-numpy1.67-dev:armel libboost-program-options1.67-dev:armel libboost-python1.67-dev:armel libboost-random1.67-dev:armel libboost-regex1.67-dev:armel libboost-serialization1.67-dev:armel libboost-signals1.67-dev:armel libboost-stacktrace1.67-dev:armel libboost-system1.67-dev:armel libboost-test1.67-dev:armel libboost-thread1.67-dev:armel libboost-timer1.67-dev:armel libboost-type-erasure1.67-dev:armel libboost-wave1.67-dev:armel libboost1.67-tools-dev:armel libmpfrc++-dev:armel libntl-dev:armel glibc-doc:armel libc-l10n:armel locales:armel glibc-doc manpages-dev:armel krb5-doc krb5-user libhdf5-doc:armel libstdc++-9-doc libstdc++-9-doc:armel libsuperlu-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armel ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libsasl2-modules libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdmainutils build-essential cmake cmake-data cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base hdf5-helpers:armel intltool-debian libaec-dev:armel libaec0:armel libarchive-zip-perl libarchive13 libarmadillo-dev:armel libarmadillo9:armel libarpack2:armel libarpack2-dev:armel libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbamtools-dev:armel libbamtools2.5.1:armel libblas-dev:armel libblas3:armel libboost-math-dev:armel libboost-math1.67-dev:armel libboost-math1.67.0:armel libboost1.67-dev:armel libbrotli1 libbsd0 libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdisorder-dev:armel libdisorder0:armel libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgfortran5:armel libglib2.0-0 libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2 libhdf5-103:armel libhdf5-cpp-103:armel libhdf5-dev:armel libicu63 libio-string-perl libjpeg62-turbo:armel libjpeg62-turbo-dev:armel libjsoncpp-dev:armel libjsoncpp1 libjsoncpp1:armel libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:armel liblapack3:armel libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:armel libsmithwaterman0:armel libssh2-1 libssl1.1 libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libsuperlu-dev:armel libsuperlu5:armel libsz2:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libuv1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db po-debconf procps sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel 0 upgraded, 154 newly installed, 0 to remove and 0 not upgraded. Need to get 110 MB of archives. After this operation, 551 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [960 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 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 1.22.4-4 [919 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.1-1 [1308 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main armel gcc-10-base armel 10-20200222-1 [195 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.2.1-30 [196 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.2-1 [102 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libprocps8 amd64 2:3.3.16-3 [62.6 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 procps amd64 2:3.3.16-3 [262 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.34-4 [2744 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.15-1 [104 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.29-10 [2638 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.2.1-30 [1697 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.2.1-30 [10.7 MB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 cmake-data all 3.16.3-1 [1628 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-4 [709 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive13 amd64 3.4.0-1+b1 [335 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libbrotli1 amd64 1.0.7-6 [266 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5support0 amd64 1.17-6 [64.6 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libk5crypto3 amd64 1.17-6 [116 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5-3 amd64 1.17-6 [366 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-6 [156 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [69.0 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [106 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-common all 2.4.49+dfsg-1 [91.9 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-1 [226 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libnghttp2-14 amd64 1.40.0-1 [85.0 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b1 [60.8 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libcurl4 amd64 7.68.0-1 [321 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3.1 [77.6 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 librhash0 amd64 1.3.9-1 [123 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libuv1 amd64 1.34.2-1 [127 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 cmake amd64 3.16.3-1 [3673 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.2.1-28cross1 [195 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [6813 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-28cross1 [191 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10-20200211-1cross1 [191 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.29-9cross1 [1128 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 10-20200211-1cross1 [38.3 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 10-20200211-1cross1 [85.0 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 10-20200211-1cross1 [8668 B] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.2.1-28cross1 [340 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 10-20200211-1cross1 [369 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 10-20200211-1cross1 [114 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.2.1-28cross1 [643 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [7165 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.4.8-1cross1 [1128 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.29-9cross1 [2141 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.2.1-28cross1 [1710 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.2.1-28cross1 [7394 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000002-1 [52.0 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-13 [513 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-2 [104 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.5-1 [1320 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.9 [994 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armel hdf5-helpers armel 1.10.4+repack-11 [35.3 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 10-20200222-1 [38.3 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.15-1 [101 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.29-10 [2338 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main armel libaec0 armel 1.0.4-1 [19.8 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main armel libsz2 armel 1.0.4-1 [6692 B] Get:114 http://debian.oregonstate.edu/debian unstable/main armel libaec-dev armel 1.0.4-1 [17.8 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main armel libblas3 armel 3.9.0-1 [176 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main armel libgfortran5 armel 10-20200222-1 [245 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main armel liblapack3 armel 3.9.0-1 [2173 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main armel libarpack2 armel 3.7.0-3 [102 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 10-20200222-1 [408 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main armel libsuperlu5 armel 5.2.1+dfsg1-4 [155 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main armel libarmadillo9 armel 1:9.800.4+dfsg-1 [93.4 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main armel libblas-dev armel 3.9.0-1 [184 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main armel liblapack-dev armel 3.9.0-1 [4287 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main armel libarpack2-dev armel 3.7.0-3 [124 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-2 [84.7 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main armel libhdf5-103 armel 1.10.4+repack-11 [1285 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.4.19-1 [1057 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.15-1 [120 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.29-10 [2184 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-2 [185 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main armel libjpeg62-turbo armel 1:1.5.2-2+b1 [112 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main armel libjpeg62-turbo-dev armel 1:1.5.2-2+b1 [182 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main armel libhdf5-cpp-103 armel 1.10.4+repack-11 [125 kB] Get:134 http://debian.oregonstate.edu/debian unstable/main armel libhdf5-dev armel 1.10.4+repack-11 [2516 kB] Get:135 http://debian.oregonstate.edu/debian unstable/main armel libsuperlu-dev armel 5.2.1+dfsg1-4 [18.4 kB] Get:136 http://debian.oregonstate.edu/debian unstable/main armel libarmadillo-dev armel 1:9.800.4+dfsg-1 [379 kB] Get:137 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.2.1-30 [347 kB] Get:138 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 10-20200222-1 [8852 B] Get:139 http://debian.oregonstate.edu/debian unstable/main armel libbamtools2.5.1 armel 2.5.1+dfsg-5 [134 kB] Get:140 http://debian.oregonstate.edu/debian unstable/main armel libbamtools-dev armel 2.5.1+dfsg-5 [22.1 kB] Get:141 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 10-20200222-1 [86.8 kB] Get:142 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 10-20200222-1 [115 kB] Get:143 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.2.1-30 [645 kB] Get:144 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.2.1-30 [1741 kB] Get:145 http://debian.oregonstate.edu/debian unstable/main armel libboost1.67-dev armel 1.67.0-17 [8389 kB] Get:146 http://debian.oregonstate.edu/debian unstable/main armel libboost-math1.67.0 armel 1.67.0-17 [368 kB] Get:147 http://debian.oregonstate.edu/debian unstable/main armel libboost-math1.67-dev armel 1.67.0-17 [520 kB] Get:148 http://debian.oregonstate.edu/debian unstable/main armel libboost-math-dev armel 1.67.0.2+b1 [4472 B] Get:149 http://debian.oregonstate.edu/debian unstable/main armel libdisorder0 armel 0.0.2+git20130809.8062ee1-1 [6180 B] Get:150 http://debian.oregonstate.edu/debian unstable/main armel libdisorder-dev armel 0.0.2+git20130809.8062ee1-1 [4164 B] Get:151 http://debian.oregonstate.edu/debian unstable/main armel libjsoncpp1 armel 1.7.4-3.1 [66.2 kB] Get:152 http://debian.oregonstate.edu/debian unstable/main armel libjsoncpp-dev armel 1.7.4-3.1 [83.8 kB] Get:153 http://debian.oregonstate.edu/debian unstable/main armel libsmithwaterman0 armel 0.0+git20160702.2610e25-7 [30.5 kB] Get:154 http://debian.oregonstate.edu/debian unstable/main armel libsmithwaterman-dev armel 0.0+git20160702.2610e25-7 [35.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 110 MB in 1s (77.2 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12785 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.1-1_amd64.deb ... Unpacking man-db (2.9.1-1) ... 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Selecting previously unselected package sensible-utils. Preparing to unpack .../012-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../013-libmagic-mgc_1%3a5.38-4_amd64.deb ... Unpacking libmagic-mgc (1:5.38-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../014-libmagic1_1%3a5.38-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.38-4) ... Selecting previously unselected package file. Preparing to unpack .../015-file_1%3a5.38-4_amd64.deb ... Unpacking file (1:5.38-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../016-gettext-base_0.19.8.1-10_amd64.deb ... Unpacking gettext-base (0.19.8.1-10) ... Selecting previously unselected package ucf. Preparing to unpack .../017-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../018-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../019-m4_1.4.18-4_amd64.deb ... Unpacking m4 (1.4.18-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../020-autoconf_2.69-11.1_all.deb ... Unpacking autoconf (2.69-11.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../021-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../022-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../023-autopoint_0.19.8.1-10_all.deb ... Unpacking autopoint (0.19.8.1-10) ... Selecting previously unselected package binutils-arm-linux-gnueabi. 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Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../048-librtmp1_2.4+20151223.gitfa8646d.1-2+b1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../049-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../050-libcurl4_7.68.0-1_amd64.deb ... Unpacking libcurl4:amd64 (7.68.0-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../051-libexpat1_2.2.9-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../052-libjsoncpp1_1.7.4-3.1_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3.1) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../053-librhash0_1.3.9-1_amd64.deb ... Unpacking librhash0:amd64 (1.3.9-1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../054-libuv1_1.34.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.34.2-1) ... Selecting previously unselected package cmake. Preparing to unpack .../055-cmake_3.16.3-1_amd64.deb ... Unpacking cmake (3.16.3-1) ... Selecting previously unselected package gcc-9-arm-linux-gnueabi-base:amd64. Preparing to unpack .../056-gcc-9-arm-linux-gnueabi-base_9.2.1-28cross1_amd64.deb ... Unpacking gcc-9-arm-linux-gnueabi-base:amd64 (9.2.1-28cross1) ... Selecting previously unselected package cpp-9-arm-linux-gnueabi. Preparing to unpack .../057-cpp-9-arm-linux-gnueabi_9.2.1-28cross1_amd64.deb ... Unpacking cpp-9-arm-linux-gnueabi (9.2.1-28cross1) ... Selecting previously unselected package cpp-arm-linux-gnueabi. Preparing to unpack .../058-cpp-arm-linux-gnueabi_4%3a9.2.1-3.1_amd64.deb ... Unpacking cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Selecting previously unselected package cross-config. 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Setting up liblocale-gettext-perl (1.07-4) ... Setting up libprocps8:amd64 (2:3.3.16-3) ... Setting up libjsoncpp1:amd64 (1.7.4-3.1) ... Setting up gcc-9-base:armel (9.2.1-30) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libgomp1-armel-cross (10-20200211-1cross1) ... Setting up libstdc++-9-dev:amd64 (9.2.1-30) ... Setting up libtool (2.4.6-13) ... Setting up libarchive13:amd64 (3.4.0-1+b1) ... Setting up libgcc-s1-armel-cross (10-20200211-1cross1) ... Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up libstdc++6-armel-cross (10-20200211-1cross1) ... Setting up libatomic1-armel-cross (10-20200211-1cross1) ... Setting up libasan5-armel-cross (9.2.1-28cross1) ... Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libubsan1-armel-cross (10-20200211-1cross1) ... 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 (1.17-6) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up g++-9 (9.2.1-30) ... Setting up libgcc-9-dev-armel-cross (9.2.1-28cross1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up procps (2:3.3.16-3) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up build-essential (12.8) ... Setting up libcurl4:amd64 (7.68.0-1) ... 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 gettext (0.19.8.1-10) ... Setting up libstdc++-9-dev-armel-cross (9.2.1-28cross1) ... Setting up gcc-9-arm-linux-gnueabi (9.2.1-28cross1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+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 g++-9-arm-linux-gnueabi (9.2.1-28cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-libxml-perl (2.0134+dfsg-2) ... 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 gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up cmake (3.16.3-1) ... Setting up po-debconf (1.0.21) ... Setting up g++-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armel (12.8) ... Setting up libcrypt1:armel (1:4.4.15-1) ... Setting up libgcc-s1:armel (10-20200222-1) ... Setting up dh-autoreconf (19) ... Setting up libc6:armel (2.29-10) ... Setting up libcrypt-dev:armel (1:4.4.15-1) ... Setting up libc6-dev:armel (2.29-10) ... Setting up libstdc++6:armel (10-20200222-1) ... Setting up libjsoncpp1:armel (1.7.4-3.1) ... Setting up libdisorder0:armel (0.0.2+git20130809.8062ee1-1) ... Setting up libjsoncpp-dev:armel (1.7.4-3.1) ... Setting up libsmithwaterman0:armel (0.0+git20160702.2610e25-7) ... Setting up debhelper (12.9) ... Setting up zlib1g:armel (1:1.2.11.dfsg-2) ... Setting up libboost-math1.67.0:armel (1.67.0-17) ... Setting up libgomp1:armel (10-20200222-1) ... Setting up libaec0:armel (1.0.4-1) ... Setting up libasan5:armel (9.2.1-30) ... Setting up libblas3:armel (3.9.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabi/libblas.so.3 (libblas.so.3-arm-linux-gnueabi) in auto mode Setting up libjpeg62-turbo:armel (1:1.5.2-2+b1) ... Setting up libjpeg62-turbo-dev:armel (1:1.5.2-2+b1) ... Setting up libbamtools2.5.1:armel (2.5.1+dfsg-5) ... Setting up libatomic1:armel (10-20200222-1) ... Setting up libdisorder-dev:armel (0.0.2+git20130809.8062ee1-1) ... Setting up libgfortran5:armel (10-20200222-1) ... Setting up libubsan1:armel (10-20200222-1) ... Setting up zlib1g-dev:armel (1:1.2.11.dfsg-2) ... Setting up libblas-dev:armel (3.9.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/blas/libblas.so to provide /usr/lib/arm-linux-gnueabi/libblas.so (libblas.so-arm-linux-gnueabi) in auto mode Setting up libsz2:armel (1.0.4-1) ... Setting up liblapack3:armel (3.9.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabi/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabi) in auto mode Setting up libaec-dev:armel (1.0.4-1) ... Setting up libarpack2:armel (3.7.0-3) ... Setting up libsuperlu5:armel (5.2.1+dfsg1-4) ... Setting up libgcc-9-dev:armel (9.2.1-30) ... Setting up libbamtools-dev:armel (2.5.1+dfsg-5) ... Setting up libhdf5-103:armel (1.10.4+repack-11) ... Setting up liblapack-dev:armel (3.9.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabi/liblapack.so (liblapack.so-arm-linux-gnueabi) in auto mode Setting up libsmithwaterman-dev:armel (0.0+git20160702.2610e25-7) ... Setting up libarmadillo9:armel (1:9.800.4+dfsg-1) ... Setting up libsuperlu-dev:armel (5.2.1+dfsg1-4) ... Setting up libarpack2-dev:armel (3.7.0-3) ... Setting up libstdc++-9-dev:armel (9.2.1-30) ... Setting up libhdf5-cpp-103:armel (1.10.4+repack-11) ... Setting up libhdf5-dev:armel (1.10.4+repack-11) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabi/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libboost1.67-dev:armel (1.67.0-17) ... Setting up libboost-math1.67-dev:armel (1.67.0-17) ... Setting up libboost-math-dev:armel (1.67.0.2+b1) ... Setting up libarmadillo-dev:armel (1:9.800.4+dfsg-1) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-4 dpkg-dev_1.19.7 g++-9_9.2.1-30 gcc-8_8.3.0-29 gcc-9_9.2.1-30 libc6-dev_2.29-10 libstdc++-9-dev_9.2.1-30 libstdc++-9-dev-armel-cross_9.2.1-28cross1 libstdc++6_10-20200222-1 libstdc++6-armel-cross_10-20200211-1cross1 linux-libc-dev_5.4.19-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-4 binutils-arm-linux-gnueabi_2.34-4 binutils-common_2.34-4 binutils-x86-64-linux-gnu_2.34-4 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 cmake_3.16.3-1 cmake-data_3.16.3-1 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-29 cpp-9_9.2.1-30 cpp-9-arm-linux-gnueabi_9.2.1-28cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-30 g++-9-arm-linux-gnueabi_9.2.1-28cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10-20200222-1 gcc-10-cross-base_10-20200211-1cross1 gcc-8_8.3.0-29 gcc-8-base_8.3.0-29 gcc-9_9.2.1-30 gcc-9-arm-linux-gnueabi_9.2.1-28cross1 gcc-9-arm-linux-gnueabi-base_9.2.1-28cross1 gcc-9-base_9.2.1-30 gcc-9-cross-base_9.2.1-28cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.19-2 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-1 hdf5-helpers_1.10.4+repack-11 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-2 libarchive13_3.4.0-1+b1 libarmadillo-dev_1:9.800.4+dfsg-1 libarmadillo9_1:9.800.4+dfsg-1 libarpack2_3.7.0-3 libarpack2-dev_3.7.0-3 libasan5_9.2.1-30 libasan5-armel-cross_9.2.1-28cross1 libatomic1_10-20200222-1 libatomic1-armel-cross_10-20200211-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbamtools-dev_2.5.1+dfsg-5 libbamtools2.5.1_2.5.1+dfsg-5 libbinutils_2.34-4 libblas-dev_3.9.0-1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libboost-math-dev_1.67.0.2+b1 libboost-math1.67-dev_1.67.0-17 libboost-math1.67.0_1.67.0-17 libboost1.67-dev_1.67.0-17 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-armel-cross_2.29-9cross1 libc6-dev_2.29-10 libc6-dev-armel-cross_2.29-9cross1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200222-1 libcom-err2_1.45.5-2 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000002-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.15-1 libcrypt1_1:4.4.15-1 libctf-nobfd0_2.34-4 libctf0_2.34-4 libcurl4_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 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_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libffi7_3.3-3 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.3-2 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-29 libgcc-9-dev_9.2.1-30 libgcc-9-dev-armel-cross_9.2.1-28cross1 libgcc-s1_10-20200222-1 libgcc-s1-armel-cross_10-20200211-1cross1 libgcc1_1:10-20200222-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10-20200222-1 libglib2.0-0_2.62.5-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_10-20200222-1 libgomp1-armel-cross_10-20200211-1cross1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-6 libhdf5-103_1.10.4+repack-11 libhdf5-cpp-103_1.10.4+repack-11 libhdf5-dev_1.10.4+repack-11 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10-20200222-1 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjsoncpp-dev_1.7.4-3.1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-6 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6 libkrb5support0_1.17-6 liblapack-dev_3.9.0-1 liblapack3_3.9.0-1 libldap-2.4-2_2.4.49+dfsg-1 libldap-common_2.4.49+dfsg-1 liblocale-gettext-perl_1.07-4 liblsan0_10-20200222-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-29 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libprocps8_2:3.3.16-3 libpsl5_0.20.2-2 libquadmath0_10-20200222-1 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsmithwaterman-dev_0.0+git20160702.2610e25-7 libsmithwaterman0_0.0+git20160702.2610e25-7 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-30 libstdc++-9-dev-armel-cross_9.2.1-28cross1 libstdc++6_10-20200222-1 libstdc++6-armel-cross_10-20200211-1cross1 libsub-override-perl_0.09-2 libsuperlu-dev_5.2.1+dfsg1-4 libsuperlu5_5.2.1+dfsg1-4 libsystemd0_244.3-1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-13 libtsan0_10-20200222-1 libubsan1_10-20200222-1 libubsan1-armel-cross_10-20200211-1cross1 libuchardet0_0.0.6-3 libudev1_244.3-1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.34.2-1 libxml-libxml-perl_2.0134+dfsg-2 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.10+dfsg-4 libyaml-perl_1.30-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.19-1 linux-libc-dev-armel-cross_5.4.8-1cross1 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 po-debconf_1.0.21 procps_2:3.3.16-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tvc Binary: tvc Architecture: any Version: 5.0.3+git20151221.80e144e+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Dominique Belhachemi , Andreas Tille Homepage: http://ioncommunity.thermofisher.com Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev Package-List: tvc deb science optional arch=any Checksums-Sha1: cd0223b1b1c96a2cc5a25fbc64e4e36a00347788 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 784aa00453ced25b09efc46ed91b140cf1dc7868 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz Checksums-Sha256: 3339f118d2fe983bc028630d5bf5238b6e91b70a85e8046a742588a6c342740c 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 8fa0c2fdd8670beb4b0ab726141010e619e4763d70ef292ab137c9bd12b9b506 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz Files: 68b468ca5054fb3260ad9de40131b632 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz be57abece3e5487df0f6939a38242aa7 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCAAwFiEEkOLSwa0Uaht+u4kdu8F+uxOW8vcFAl5bTWkSHHN0dWFydEBk ZWJpYW4ub3JnAAoJELvBfrsTlvL3Wj0P/RPA3/JDLENaPvS8Z+hQOy/cIri64NFA 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signature: No public key dpkg-source: warning: failed to verify signature on ./tvc_5.0.3+git20151221.80e144e+dfsg-3.dsc dpkg-source: info: extracting tvc in /<> 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-3.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 dpkg-source: info: applying python3.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.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 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-9133500f-fd05-4cc2-b035-763b57e3c708 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Stuart Prescott dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi 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 armel debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-arm-linux-gnueabi && 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=armv7l -DCMAKE_C_COMPILER=arm-linux-gnueabi-gcc -DCMAKE_CXX_COMPILER=arm-linux-gnueabi-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabi-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabi-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/arm-linux-gnueabi-qmake -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabi .. -- The C compiler identification is GNU 9.2.1 -- The CXX compiler identification is GNU 9.2.1 -- Check for working C compiler: /usr/bin/arm-linux-gnueabi-gcc -- Check for working C compiler: /usr/bin/arm-linux-gnueabi-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/arm-linux-gnueabi-g++ -- Check for working CXX compiler: /usr/bin/arm-linux-gnueabi-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=/<>=. -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: /<>/obj-arm-linux-gnueabi dh_auto_build -a cd obj-arm-linux-gnueabi && make -j1 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-arm-linux-gnueabi' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabi/CMakeFiles /<>/obj-arm-linux-gnueabi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-arm-linux-gnueabi' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' cd /<>/obj-arm-linux-gnueabi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= Scanning dependencies of target tvcutils make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' [ 1%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o -c /<>/VariantCaller/tvcutils/tvcutils.cpp [ 3%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -c /<>/VariantCaller/tvcutils/prepare_hotspots.cpp [ 4%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o -c /<>/VariantCaller/tvcutils/validate_bed.cpp /<>/VariantCaller/tvcutils/validate_bed.cpp: In function ‘bool load_and_validate_bed(const string&, ReferenceReader&, BedFile&, Json::Value&, bool)’: /<>/VariantCaller/tvcutils/validate_bed.cpp:861:26: warning: ‘%s’ directive writing up to 65535 bytes into a region of size 1024 [-Wformat-overflow=] 783 | fields[0] = line; | ~~~~ ...... 861 | sprintf(buffer, "%s:%ld-%ld", fields[0], bed_line.start+1, bed_line.end); | ^~ /<>/VariantCaller/tvcutils/validate_bed.cpp:861:25: note: directive argument in the range [-2147483647, 2147483647] 861 | sprintf(buffer, "%s:%ld-%ld", fields[0], bed_line.start+1, bed_line.end); | ^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from /usr/arm-linux-gnueabi/include/c++/9/cstdio:42, from /usr/arm-linux-gnueabi/include/c++/9/ext/string_conversions.h:43, from /usr/arm-linux-gnueabi/include/c++/9/bits/basic_string.h:6493, from /usr/arm-linux-gnueabi/include/c++/9/string:55, from /<>/VariantCaller/tvcutils/validate_bed.cpp:5: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 65560 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /<>/VariantCaller/tvcutils/unify_vcf.cpp In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from /<>/VariantCaller/tvcutils/unify_vcf.cpp:13: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 7%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -c /<>/VariantCaller/TargetsManager.cpp [ 9%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -c /<>/Util/OptArgs.cpp In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from /<>/Util/OptArgs.h:11, from /<>/Util/OptArgs.cpp:4: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void OptArgs::StringToDoubleVector(std::vector&, const string&, const string&, char)’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 10%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /<>/external/vcflib/Variant.cpp [ 12%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. 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CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/arm-linux-gnueabi-gcc -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /<>/external/vcflib/tabixpp/index.c [ 17%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/arm-linux-gnueabi-gcc -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /<>/external/vcflib/tabixpp/bgzf.c /<>/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’: /<>/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval 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CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' [ 20%] Built target tvcutils make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' cd /<>/obj-arm-linux-gnueabi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= Scanning dependencies of target tvcassembly make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' [ 21%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /<>/VariantCaller/IndelAssembly/IndelAssembly.cpp [ 23%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -c /<>/VariantCaller/TargetsManager.cpp [ 25%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -c /<>/VariantCaller/SampleManager.cpp [ 26%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -c /<>/Util/OptArgs.cpp In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from /<>/Util/OptArgs.h:11, from /<>/Util/OptArgs.cpp:4: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void OptArgs::StringToDoubleVector(std::vector&, const string&, const string&, char)’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 28%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o -c /<>/Util/Utils.cpp In file included from /usr/arm-linux-gnueabi/include/string.h:495, from /usr/arm-linux-gnueabi/include/c++/9/cstring:42, from /<>/Util/Utils.cpp:12: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘char* GetProcessParam(const char*, const char*)’ at /<>/Util/Utils.cpp:503:15: /usr/arm-linux-gnueabi/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/Util/Utils.cpp: In function ‘char* GetProcessParam(const char*, const char*)’: /<>/Util/Utils.cpp:503:37: note: length computed here 503 | strncpy (keyword, buf, strlen (buf)-1); | ~~~~~~~^~~~~ [ 29%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /<>/obj-arm-linux-gnueabi/IonVersion.cpp [ 31%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -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 '/<>/obj-arm-linux-gnueabi' [ 31%] Built target tvcassembly make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' cd /<>/obj-arm-linux-gnueabi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi/CMakeFiles/tvc.dir/DependInfo.cmake --color= Scanning dependencies of target tvc make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /<>/VariantCaller/VariantCaller.cpp /<>/VariantCaller/VariantCaller.cpp: In function ‘void TheSilenceOfTheArmadillos(std::ofstream&)’: /<>/VariantCaller/VariantCaller.cpp:36:9: warning: ‘void arma::set_stream_err1(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:364, from /<>/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here 90 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /<>/VariantCaller/VariantCaller.cpp:36:37: warning: ‘void arma::set_stream_err1(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ^ In file included from /usr/include/armadillo:364, from /<>/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here 90 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /<>/VariantCaller/VariantCaller.cpp:36:37: warning: ‘void arma::set_stream_err1(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ^ In file included from /usr/include/armadillo:364, from /<>/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:90:1: note: declared here 90 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /<>/VariantCaller/VariantCaller.cpp:37:9: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ^~~~~~~~~~~~~~~ In file included from /usr/include/armadillo:364, from /<>/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here 101 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /<>/VariantCaller/VariantCaller.cpp:37:37: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ^ In file included from /usr/include/armadillo:364, from /<>/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here 101 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /<>/VariantCaller/VariantCaller.cpp:37:37: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ^ In file included from /usr/include/armadillo:364, from /<>/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:101:1: note: declared here 101 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ [ 34%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /<>/VariantCaller/BAMWalkerEngine.cpp [ 35%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -c /<>/VariantCaller/OrderedBAMWriter.cpp [ 37%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /<>/VariantCaller/SampleManager.cpp [ 39%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /<>/VariantCaller/TargetsManager.cpp [ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /<>/VariantCaller/HandleVariant.cpp [ 42%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /<>/VariantCaller/HotspotReader.cpp [ 43%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /<>/VariantCaller/MetricsManager.cpp [ 45%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /<>/VariantCaller/Bookkeeping/MiscUtil.cpp [ 46%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -c /<>/VariantCaller/Bookkeeping/ExtendParameters.cpp [ 48%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /<>/VariantCaller/Bookkeeping/InputStructures.cpp In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from /<>/VariantCaller/Bookkeeping/InputStructures.h:12, from /<>/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DPTreephaser&}; _Tp = DPTreephaser; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:67, from /<>/VariantCaller/Bookkeeping/InputStructures.h:12, from /<>/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h: In constructor ‘PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ [ 50%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -c /<>/VariantCaller/Bookkeeping/VcfFormat.cpp [ 51%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /<>/VariantCaller/Reads/ExtendedReadInfo.cpp [ 53%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /<>/VariantCaller/Splice/ErrorMotifs.cpp [ 54%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /<>/VariantCaller/Splice/LocalContext.cpp [ 56%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -c /<>/VariantCaller/Splice/ClassifyVariant.cpp [ 57%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -c /<>/VariantCaller/Splice/SpliceVariantHypotheses.cpp [ 59%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o -c /<>/VariantCaller/Filter/DecisionTreeData.cpp [ 60%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -c /<>/VariantCaller/Filter/VariantAssist.cpp /<>/VariantCaller/Filter/VariantAssist.cpp: In function ‘double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)’: /<>/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] 191 | fprintf(stdout, "ref.size()=%lu; ", ref.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /<>/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] 192 | fprintf(stdout, "var.size()=%lu; ", var.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /<>/VariantCaller/Filter/VariantAssist.cpp:193:37: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] 193 | fprintf(stdout, "both.size()=%lu; ", both.size()); | ~~^ ~~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u [ 62%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -c /<>/VariantCaller/HypothesisEvaluator.cpp [ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -c /<>/VariantCaller/EnsembleEval/DiagnosticJSON.cpp [ 65%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -c /<>/VariantCaller/EnsembleEval/BiasGenerator.cpp [ 67%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g 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/<>/VariantCaller/EnsembleEval/SkewGenerator.cpp [ 70%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -c /<>/VariantCaller/EnsembleEval/PosteriorInference.cpp [ 71%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib 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-I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -c /<>/VariantCaller/EnsembleEval/StackEngine.cpp [ 75%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<>/external/vcflib/tabixpp/tabix.cpp [ 81%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o /usr/bin/arm-linux-gnueabi-gcc -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /<>/external/vcflib/tabixpp/index.c [ 82%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/arm-linux-gnueabi-gcc -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -c /<>/external/vcflib/tabixpp/bgzf.c /<>/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’: /<>/external/vcflib/tabixpp/bgzf.c:678:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 84%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /<>/external/freebayes/src/AlleleParser.cpp [ 85%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /<>/BaseCaller/PIDloop.cpp [ 87%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -c /<>/BaseCaller/DPTreephaser.cpp [ 89%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -c /<>/Calibration/LinearCalibrationModel.cpp [ 90%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -c /<>/Calibration/FlowAlignment.cpp [ 92%] Building CXX object CMakeFiles/tvc.dir/Util/OptArgs.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o -c /<>/Util/OptArgs.cpp In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from /<>/Util/OptArgs.h:11, from /<>/Util/OptArgs.cpp:4: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void OptArgs::StringToDoubleVector(std::vector&, const string&, const string&, char)’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ [ 93%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval 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CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o 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CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o CMakeFiles/tvc.dir/file-io/ion_util.c.o CMakeFiles/tvc.dir/file-io/ion_error.c.o CMakeFiles/tvc.dir/IonVersion.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' [100%] Built target tvc make[2]: Leaving directory '/<>/obj-arm-linux-gnueabi' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabi/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-arm-linux-gnueabi' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a cd obj-arm-linux-gnueabi && 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 '/<>/obj-arm-linux-gnueabi' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabi/CMakeFiles /<>/obj-arm-linux-gnueabi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-arm-linux-gnueabi' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' cd /<>/obj-arm-linux-gnueabi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' [ 20%] 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/<>/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/sse -- Installing: /<>/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /<>/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /<>/debian/tvc/usr/share/TVC/examples -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf make[1]: Leaving directory '/<>/obj-arm-linux-gnueabi' 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_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcassembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcutils contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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) 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-3_armel.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_armel.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../tvc_5.0.3+git20151221.80e144e+dfsg-3_armel.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 2020-03-02T03:40:10Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ tvc_5.0.3+git20151221.80e144e+dfsg-3_armel.changes: --------------------------------------------------- Format: 1.8 Date: Sun, 01 Mar 2020 15:57:45 +1100 Source: tvc Binary: tvc tvc-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 5.0.3+git20151221.80e144e+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Stuart Prescott Description: tvc - genetic variant caller for Ion Torrent sequencing platforms Closes: 945720 Changes: tvc (5.0.3+git20151221.80e144e+dfsg-3) unstable; urgency=medium . * Team upload. * Use Python 3 in scripts (Closes: #945720). * Add Rules-Requires-Root: no. * Update Standards-Version to 4.5.0 (no changes required). * Switch to debhelper-compat (= 12). 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Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 02 Mar 2020 03:40:10 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-6), binutils (= 2.34-4), binutils-common (= 2.34-4), binutils-x86-64-linux-gnu (= 2.34-4), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.8), bzip2 (= 1.0.8-2), cmake (= 3.16.3-1), cmake-data (= 3.16.3-1), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-8 (= 8.3.0-29), cpp-9 (= 9.2.1-30), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.9), debianutils (= 4.9.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.3-2), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-5), fdisk (= 2.34-0.1), file (= 1:5.38-4), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.2.1-30), gcc (= 4:9.2.1-3.1), gcc-10-base (= 10-20200222-1), gcc-8 (= 8.3.0-29), gcc-8-base (= 8.3.0-29), gcc-9 (= 9.2.1-30), gcc-9-base (= 9.2.1-30), gettext (= 0.19.8.1-10), gettext-base (= 0.19.8.1-10), grep (= 3.4-1), groff-base (= 1.22.4-4), gzip (= 1.10-1), hdf5-helpers (= 1.10.4+repack-11), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-6), libaec-dev (= 1.0.4-1), libaec0 (= 1.0.4-1), libarchive-zip-perl (= 1.67-2), libarchive13 (= 3.4.0-1+b1), libarmadillo-dev (= 1:9.800.4+dfsg-1), libarmadillo9 (= 1:9.800.4+dfsg-1), libarpack2 (= 3.7.0-3), libarpack2-dev (= 3.7.0-3), libasan5 (= 9.2.1-30), libatomic1 (= 10-20200222-1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2+b1), libbamtools-dev (= 2.5.1+dfsg-5), libbamtools2.5.1 (= 2.5.1+dfsg-5), libbinutils (= 2.34-4), libblas-dev (= 3.9.0-1), libblas3 (= 3.9.0-1), libblkid1 (= 2.34-0.1), libboost-math-dev (= 1.67.0.2+b1), libboost-math1.67-dev (= 1.67.0-17), libboost-math1.67.0 (= 1.67.0-17), libboost1.67-dev (= 1.67.0-17), libbrotli1 (= 1.0.7-6), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.29-10), libc-dev-bin (= 2.29-10), libc6 (= 2.29-10), libc6-dev (= 2.29-10), libcap-ng0 (= 0.7.9-2.1+b1), libcc1-0 (= 10-20200222-1), libcom-err2 (= 1.45.5-2), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.15-1), libcrypt1 (= 1:4.4.15-1), libctf-nobfd0 (= 2.34-4), libctf0 (= 2.34-4), libcurl4 (= 7.68.0-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.251), libdebhelper-perl (= 12.9), 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 (= 2.2.9-1), libfdisk1 (= 2.34-0.1), libffi7 (= 3.3-3), libfile-stripnondeterminism-perl (= 1.6.3-2), libgcc-8-dev (= 8.3.0-29), libgcc-9-dev (= 9.2.1-30), libgcc-s1 (= 10-20200222-1), libgcc1 (= 1:10-20200222-1), libgcrypt20 (= 1.8.5-5), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libgfortran5 (= 10-20200222-1), libglib2.0-0 (= 2.62.5-1), libgmp10 (= 2:6.2.0+dfsg-4), libgnutls30 (= 3.6.12-2), libgomp1 (= 10-20200222-1), libgpg-error0 (= 1.37-1), libgssapi-krb5-2 (= 1.17-6), libhdf5-103 (= 1.10.4+repack-11), libhdf5-cpp-103 (= 1.10.4+repack-11), libhdf5-dev (= 1.10.4+repack-11), libhogweed5 (= 3.5.1+really3.5.1-2), libicu63 (= 63.2-2), libidn2-0 (= 2.2.0-2), libisl22 (= 0.22.1-1), libitm1 (= 10-20200222-1), libjpeg62-turbo (= 1:1.5.2-2+b1), libjpeg62-turbo-dev (= 1:1.5.2-2+b1), libjsoncpp-dev (= 1.7.4-3.1), libjsoncpp1 (= 1.7.4-3.1), libk5crypto3 (= 1.17-6), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.17-6), libkrb5support0 (= 1.17-6), liblapack-dev (= 3.9.0-1), liblapack3 (= 3.9.0-1), libldap-2.4-2 (= 2.4.49+dfsg-1), libldap-common (= 2.4.49+dfsg-1), liblsan0 (= 10-20200222-1), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-29), libncurses6 (= 6.2-1), libncursesw6 (= 6.2-1), libnettle7 (= 3.5.1+really3.5.1-2), libnghttp2-14 (= 1.40.0-1), libp11-kit0 (= 0.23.20-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.0-9), libpipeline1 (= 1.5.2-2), libprocps8 (= 2:3.3.16-3), libpsl5 (= 0.20.2-2), libquadmath0 (= 10-20200222-1), librhash0 (= 1.3.9-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b1), libsasl2-2 (= 2.1.27+dfsg-2), libsasl2-modules-db (= 2.1.27+dfsg-2), libseccomp2 (= 2.4.2-2), libselinux1 (= 3.0-1+b1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libsmithwaterman-dev (= 0.0+git20160702.2610e25-7), libsmithwaterman0 (= 0.0+git20160702.2610e25-7), libssh2-1 (= 1.8.0-2.1), libssl1.1 (= 1.1.1d-2), libstdc++-9-dev (= 9.2.1-30), libstdc++6 (= 10-20200222-1), libsub-override-perl (= 0.09-2), libsuperlu-dev (= 5.2.1+dfsg1-4), libsuperlu5 (= 5.2.1+dfsg1-4), libsystemd0 (= 244.3-1), libsz2 (= 1.0.4-1), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2-1), libtool (= 2.4.6-13), libtsan0 (= 10-20200222-1), libubsan1 (= 10-20200222-1), libuchardet0 (= 0.0.6-3), libudev1 (= 244.3-1), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libuv1 (= 1.34.2-1), libxml2 (= 2.9.10+dfsg-4), libzstd1 (= 1.4.4+dfsg-3), linux-libc-dev (= 5.4.19-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-1), ncurses-bin (= 6.2-1), patch (= 2.7.6-6), perl (= 5.30.0-9), perl-base (= 5.30.0-9), perl-modules-5.30 (= 5.30.0-9), po-debconf (= 1.0.21), procps (= 2:3.3.16-3), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-2.1), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1583038665" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_armel.deb ----------------------------------------------------- new Debian package, version 2.0. size 10328576 bytes: control archive=708 bytes. 488 bytes, 12 lines control 399 bytes, 4 lines md5sums Package: tvc-dbgsym Source: tvc Version: 5.0.3+git20151221.80e144e+dfsg-3 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 10453 Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-3) Section: debug Priority: optional Description: debug symbols for tvc Build-Ids: 7c328e2bea21bc8323bf0534ecab3ead2092495d 961a89096f5df63c6fe0f69d839d2d442ac2d68c a782b018da768014179b4513bb9e96b99cdb4d5a drwxr-xr-x root/root 0 2020-03-01 04:57 ./ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/7c/ -rw-r--r-- root/root 7019264 2020-03-01 04:57 ./usr/lib/debug/.build-id/7c/328e2bea21bc8323bf0534ecab3ead2092495d.debug drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/96/ -rw-r--r-- root/root 2434084 2020-03-01 04:57 ./usr/lib/debug/.build-id/96/1a89096f5df63c6fe0f69d839d2d442ac2d68c.debug drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/a7/ -rw-r--r-- root/root 786104 2020-03-01 04:57 ./usr/lib/debug/.build-id/a7/82b018da768014179b4513bb9e96b99cdb4d5a.debug drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.dwz/arm-linux-gnueabi/ -rw-r--r-- root/root 447980 2020-03-01 04:57 ./usr/lib/debug/.dwz/arm-linux-gnueabi/tvc.debug drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-03-01 04:57 ./usr/share/doc/tvc-dbgsym -> tvc tvc_5.0.3+git20151221.80e144e+dfsg-3_armel.deb ---------------------------------------------- new Debian package, version 2.0. size 969816 bytes: control archive=1680 bytes. 992 bytes, 16 lines control 2459 bytes, 28 lines md5sums Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-3 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 3077 Depends: libarmadillo9 (>= 1:9.800.4+dfsg), libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.29), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 3.5), libjsoncpp1 (>= 1.7.4), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), python3 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 2020-03-01 04:57 ./ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/bin/ -rwxr-xr-x root/root 970976 2020-03-01 04:57 ./usr/bin/tvc -rwxr-xr-x root/root 178624 2020-03-01 04:57 ./usr/bin/tvcassembly -rwxr-xr-x root/root 551868 2020-03-01 04:57 ./usr/bin/tvcutils -rwxr-xr-x root/root 12985 2020-03-01 04:57 ./usr/bin/variant_caller_pipeline.py drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/examples/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/TVC/examples/example1/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./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 2020-03-01 04:57 ./usr/share/TVC/pluginMedia/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./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 2020-03-01 04:57 ./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 2020-03-01 04:57 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/doc/tvc/ -rw-r--r-- root/root 1078 2020-03-01 04:46 ./usr/share/doc/tvc/README.Debian -rw-r--r-- root/root 1180 2020-03-01 04:57 ./usr/share/doc/tvc/changelog.Debian.gz -rw-r--r-- root/root 2939 2020-03-01 04:46 ./usr/share/doc/tvc/copyright drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/lintian/ drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 135 2020-03-01 04:46 ./usr/share/lintian/overrides/tvc lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [577 B] Get:5 copy:/<>/apt_archive ./ Packages [663 B] Fetched 2203 B in 0s (114 kB/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 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdevel-size-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl libjson-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libxml-parser-perl libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-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 libjson-xs-perl libfreezethaw-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libperl4-corelibs-perl libauthen-sasl-perl libpackage-stash-xs-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdevel-size-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl libjson-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armel t1utils 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 7896 kB of archives. After this operation, 22.8 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-4 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 6.1 [19.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.63-1 [35.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.19-2 [529 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.31.1-3 [661 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.19-2 [889 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b2 [71.3 kB] Get:11 http://debian.oregonstate.edu/debian 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amd64 libio-pty-perl amd64 1:1.12-1 [36.3 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-2 [101 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-perl all 4.02000-2 [88.8 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libmldbm-perl all 2.05-2 [18.4 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003006-1 [58.7 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1 [10.2 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.008001-2 [331 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.81+repack-1 [35.4 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.55.0 [1312 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7896 kB in 0s (30.2 MB/s) Selecting previously unselected package readline-common. (Reading database ... 38685 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-4_all.deb ... Unpacking readline-common (8.0-4) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-4_amd64.deb ... Unpacking libreadline8:amd64 (8.0-4) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.1_all.deb ... Unpacking netbase (6.1) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.63-1_amd64.deb ... Unpacking diffstat (1.63-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.19-2_amd64.deb ... Unpacking gpgconf (2.2.19-2) ... Selecting previously unselected package libsqlite3-0:amd64. 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Setting up patchutils (0.3.4-2+b1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.26-1) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up t1utils (1.41-3) ... Setting up liblinux-epoll-perl (0.017-1) ... Setting up diffstat (1.63-1) ... Setting up libvariable-magic-perl (0.62-1+b2) ... Setting up libb-hooks-op-check-perl (0.22-1+b2) ... Setting up libipc-run-perl (20180523.0-2) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3100-1) ... Setting up libsub-name-perl (0.26-1) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up libjson-perl (4.02000-2) ... Setting up librole-tiny-perl (2.001004-1) ... Setting up netbase (6.1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b3) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libfont-ttf-perl (1.06-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (8.0-4) ... Setting up liburi-perl (1.76-2) ... Setting up libnet-ssleay-perl (1.88-2) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b5) ... Setting up libreadline8:amd64 (8.0-4) ... Setting up libtype-tiny-perl (1.008001-2) ... Setting up libnet-dns-perl (1.22-1) ... Setting up libdevel-callchecker-perl (0.008-1+b1) ... Setting up libio-async-loop-epoll-perl (0.20-1) ... Setting up libhtml-parser-perl (3.72-5) ... Setting up gpgconf (2.2.19-2) ... Setting up libio-socket-ssl-perl (2.067-1) ... Setting up gpg (2.2.19-2) ... Setting up libparams-classify-perl (0.015-1+b2) ... Setting up libcgi-pm-perl (4.46-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libmailtools-perl (2.21-1) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libemail-valid-perl (1.202-1) ... Setting up libpackage-stash-perl (0.38-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.003006-1) ... Setting up libmoox-aliases-perl (0.001006-1) ... Setting up libb-hooks-endofscope-perl (0.24-1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.55.0) ... Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ... Processing triggers for man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.29-10) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 150548 Build-Time: 237 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 24 Job: tvc_5.0.3+git20151221.80e144e+dfsg-3 Lintian: pass Machine Architecture: amd64 Package: tvc Package-Time: 271 Source-Version: 5.0.3+git20151221.80e144e+dfsg-3 Space: 150548 Status: successful Version: 5.0.3+git20151221.80e144e+dfsg-3 -------------------------------------------------------------------------------- Finished at 2020-03-02T03:40:10Z Build needed 00:04:31, 150548k disk space