sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | tvc 5.0.3+git20151221.80e144e+dfsg-3 (arm64) Mon, 29 Mar 2021 09:15:44 +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: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-5112abf9-b26a-4c97-9e97-be98462e60b5' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-t3hdSg/resolver-RcWz01' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [154 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [63.6 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-03-29-0800.22-F-2021-03-29-0800.22.pdiff [1430 B] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-03-29-0800.22-F-2021-03-29-0800.22.pdiff [1430 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-03-29-0800.22-F-2021-03-29-0800.22.pdiff [1057 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-03-29-0800.22-F-2021-03-29-0800.22.pdiff [1057 B] Get:6 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8483 kB] Fetched 8766 kB in 3s (3174 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 (7064 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/tvc-t3hdSg/tvc-5.0.3+git20151221.80e144e+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-t3hdSg' 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-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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 [441 B] Get:5 copy:/<>/apt_archive ./ Packages [533 B] Fetched 1931 B in 0s (81.2 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-aarch64-linux-gnu bsdextrautils build-essential cmake cmake-data cpp-10-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-10 g++-10-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-10-aarch64-linux-gnu gcc-10-aarch64-linux-gnu-base gcc-10-base:arm64 gcc-10-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base hdf5-helpers:arm64 intltool-debian libaec-dev:arm64 libaec0:arm64 libarchive-zip-perl libarchive13 libarmadillo-dev:arm64 libarmadillo10:arm64 libarpack2:arm64 libarpack2-dev:arm64 libasan6:arm64 libasan6-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbamtools-dev:arm64 libbamtools2.5.1:arm64 libblas-dev:arm64 libblas3:arm64 libboost-math-dev:arm64 libboost-math1.74-dev:arm64 libboost-math1.74.0:arm64 libboost1.74-dev:arm64 libbrotli1 libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64 libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdisorder-dev:arm64 libdisorder0:arm64 libdpkg-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:arm64 libgcc-10-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgfortran5:arm64 libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhdf5-103-1:arm64 libhdf5-cpp-103-1:arm64 libhdf5-dev:arm64 libhdf5-fortran-102:arm64 libhdf5-hl-100:arm64 libhdf5-hl-cpp-100:arm64 libhdf5-hl-fortran-100:arm64 libicu67 libio-string-perl libitm1:arm64 libitm1-arm64-cross libjpeg-dev:arm64 libjpeg62-turbo:arm64 libjpeg62-turbo-dev:arm64 libjsoncpp-dev:arm64 libjsoncpp24 libjsoncpp24:arm64 libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 liblapack-dev:arm64 liblapack3:arm64 libldap-2.4-2 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libnsl-dev libnsl-dev:arm64 libnsl2:arm64 libperl5.32 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:arm64 libsmithwaterman0:arm64 libssh2-1 libssl1.1:arm64 libstdc++-10-dev libstdc++-10-dev:arm64 libstdc++-10-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libsuperlu-dev:arm64 libsuperlu5:arm64 libsz2:arm64 libtirpc-dev libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-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:arm64 linux-libc-dev-arm64-cross m4 man-db perl perl-modules-5.32 po-debconf procps sensible-utils ucf zlib1g:arm64 zlib1g-dev:arm64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc ninja-build gcc-10-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-10-multilib gcc-10-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libitpp-dev:arm64 libbamtools-doc:arm64 liblapack-doc:arm64 libboost1.74-doc:arm64 libboost-atomic1.74-dev:arm64 libboost-chrono1.74-dev:arm64 libboost-container1.74-dev:arm64 libboost-context1.74-dev:arm64 libboost-contract1.74-dev:arm64 libboost-coroutine1.74-dev:arm64 libboost-date-time1.74-dev:arm64 libboost-exception1.74-dev:arm64 libboost-fiber1.74-dev:arm64 libboost-filesystem1.74-dev:arm64 libboost-graph1.74-dev:arm64 libboost-graph-parallel1.74-dev:arm64 libboost-iostreams1.74-dev:arm64 libboost-locale1.74-dev:arm64 libboost-log1.74-dev:arm64 libboost-mpi1.74-dev:arm64 libboost-mpi-python1.74-dev:arm64 libboost-numpy1.74-dev:arm64 libboost-program-options1.74-dev:arm64 libboost-python1.74-dev:arm64 libboost-random1.74-dev:arm64 libboost-regex1.74-dev:arm64 libboost-serialization1.74-dev:arm64 libboost-stacktrace1.74-dev:arm64 libboost-system1.74-dev:arm64 libboost-test1.74-dev:arm64 libboost-thread1.74-dev:arm64 libboost-timer1.74-dev:arm64 libboost-type-erasure1.74-dev:arm64 libboost-wave1.74-dev:arm64 libboost1.74-tools-dev:arm64 libmpfrc++-dev:arm64 libntl-dev:arm64 libboost-nowide1.74-dev:arm64 glibc-doc:arm64 libc-l10n:arm64 locales:arm64 glibc-doc manpages-dev:arm64 gnupg git bzr krb5-doc:arm64 krb5-user:arm64 libhdf5-doc:arm64 libstdc++-10-doc libstdc++-10-doc:arm64 libsuperlu-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl Recommended packages: gnupg libalgorithm-merge-perl curl | wget | lynx libidn2-0:arm64 libnss-nis:arm64 libnss-nisplus:arm64 ca-certificates libfile-fcntllock-perl libarchive-cpio-perl krb5-locales:arm64 libldap-common libgpm2 publicsuffix libsasl2-modules libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils build-essential cmake cmake-data cpp-10-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-10 g++-10-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-10-aarch64-linux-gnu gcc-10-aarch64-linux-gnu-base gcc-10-base:arm64 gcc-10-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base hdf5-helpers:arm64 intltool-debian libaec-dev:arm64 libaec0:arm64 libarchive-zip-perl libarchive13 libarmadillo-dev:arm64 libarmadillo10:arm64 libarpack2:arm64 libarpack2-dev:arm64 libasan6:arm64 libasan6-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbamtools-dev:arm64 libbamtools2.5.1:arm64 libblas-dev:arm64 libblas3:arm64 libboost-math-dev:arm64 libboost-math1.74-dev:arm64 libboost-math1.74.0:arm64 libboost1.74-dev:arm64 libbrotli1 libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64 libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdisorder-dev:arm64 libdisorder0:arm64 libdpkg-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:arm64 libgcc-10-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgfortran5:arm64 libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhdf5-103-1:arm64 libhdf5-cpp-103-1:arm64 libhdf5-dev:arm64 libhdf5-fortran-102:arm64 libhdf5-hl-100:arm64 libhdf5-hl-cpp-100:arm64 libhdf5-hl-fortran-100:arm64 libicu67 libio-string-perl libitm1:arm64 libitm1-arm64-cross libjpeg-dev:arm64 libjpeg62-turbo:arm64 libjpeg62-turbo-dev:arm64 libjsoncpp-dev:arm64 libjsoncpp24 libjsoncpp24:arm64 libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 liblapack-dev:arm64 liblapack3:arm64 libldap-2.4-2 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libnsl-dev libnsl-dev:arm64 libnsl2:arm64 libperl5.32 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:arm64 libsmithwaterman0:arm64 libssh2-1 libssl1.1:arm64 libstdc++-10-dev libstdc++-10-dev:arm64 libstdc++-10-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libsuperlu-dev:arm64 libsuperlu5:arm64 libsz2:arm64 libtirpc-dev libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan0-arm64-cross libubsan1:arm64 libubsan1-arm64-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:arm64 linux-libc-dev-arm64-cross m4 man-db perl perl-modules-5.32 po-debconf procps sbuild-build-depends-main-dummy:arm64 sensible-utils ucf zlib1g:arm64 zlib1g-dev:arm64 0 upgraded, 171 newly installed, 0 to remove and 0 not upgraded. Need to get 259 MB of archives. After this operation, 1272 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 bsdextrautils amd64 2.36.1-7 [145 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.32 all 5.32.1-3 [2823 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.32 amd64 5.32.1-3 [4110 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.32.1-3 [293 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-10-base arm64 10.2.1-6 [201 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libprocps8 amd64 2:3.3.17-4 [63.8 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 procps amd64 2:3.3.17-4 [501 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.39-3 [69.1 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-14 [313 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.3-2 [814 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.21-4 [510 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.35.2-2 [2813 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.18-2 [104 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libtirpc-dev amd64 1.3.1-1 [190 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.31-10 [2344 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev amd64 10.2.1-6 [1741 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10 amd64 10.2.1-6 [9380 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:10.2.1-1 [1644 B] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.7.1 [1537 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.7.1 [2149 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.9 [7704 B] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 cmake-data all 3.18.4-2 [1725 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-6 [8625 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-6.3+b1 [693 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-2 [232 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libssh2-1 amd64 1.9.0-3 [169 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libcurl4 amd64 7.74.0-1.1 [341 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libuv1 amd64 1.40.0-1 [132 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 cmake amd64 3.18.4-2 [5593 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-aarch64-linux-gnu-base amd64 10.2.1-6cross1 [202 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-10-aarch64-linux-gnu amd64 10.2.1-6cross1 [46.6 MB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:10.2.1-1 [16.8 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.17 [31.4 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10.2.1-6cross1 [197 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.31-9cross4 [1233 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-arm64-cross all 10.2.1-6cross1 [34.5 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 10.2.1-6cross1 [89.5 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 10.2.1-6cross1 [23.4 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 10.2.1-6cross1 [9240 B] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libasan6-arm64-cross all 10.2.1-6cross1 [1994 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 10.2.1-6cross1 [793 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 10.2.1-6cross1 [1949 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 10.2.1-6cross1 [410 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 10.2.1-6cross1 [759 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-10-dev-arm64-cross all 10.2.1-6cross1 [880 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-aarch64-linux-gnu amd64 10.2.1-6cross1 [53.2 MB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:10.2.1-1 [1460 B] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 5.10.13-1cross4 [1375 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.31-9cross4 [2030 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev-arm64-cross all 10.2.1-6cross1 [1682 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10-aarch64-linux-gnu amd64 10.2.1-6cross1 [49.7 MB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:10.2.1-1 [1176 B] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 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+b1 [337 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 0.44-1.1 [19.0 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 1.006-1 [43.8 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.17 [30.4 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.17 [41.4 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.9 [6708 B] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-15 [513 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [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 1.11.0-1 [25.6 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.183-3 [165 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.21-4 [1311 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.3.4 [1049 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main arm64 hdf5-helpers arm64 1.10.6+repack-2 [40.0 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-s1 arm64 10.2.1-6 [34.6 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt1 arm64 1:4.4.18-2 [89.4 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.31-10 [2456 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main arm64 libaec0 arm64 1.0.4-1 [19.8 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main arm64 libsz2 arm64 1.0.4-1 [6736 B] Get:112 http://debian.oregonstate.edu/debian unstable/main arm64 libaec-dev arm64 1.0.4-1 [18.2 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main arm64 libblas3 arm64 3.9.0-3 [101 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main arm64 liblapack3 arm64 3.9.0-3 [1541 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main arm64 libarpack2 arm64 3.8.0-1 [84.2 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 10.2.1-6 [451 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main arm64 libsuperlu5 arm64 5.2.2+dfsg1-2 [133 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main arm64 libarmadillo10 arm64 1:10.1.2+dfsg-5 [97.9 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main arm64 libblas-dev arm64 3.9.0-3 [107 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main arm64 liblapack-dev arm64 3.9.0-3 [2758 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main arm64 libarpack2-dev arm64 3.8.0-1 [101 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main arm64 zlib1g arm64 1:1.2.11.dfsg-2 [87.9 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main arm64 libhdf5-103-1 arm64 1.10.6+repack-2 [1029 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main arm64 libhdf5-fortran-102 arm64 1.10.6+repack-2 [101 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main arm64 libhdf5-hl-100 arm64 1.10.6+repack-2 [78.3 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main arm64 libhdf5-hl-fortran-100 arm64 1.10.6+repack-2 [53.7 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main arm64 libhdf5-cpp-103-1 arm64 1.10.6+repack-2 [134 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main arm64 libhdf5-hl-cpp-100 arm64 1.10.6+repack-2 [37.2 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 5.10.26-1 [1293 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt-dev arm64 1:4.4.18-2 [109 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main arm64 libcom-err2 arm64 1.46.2-1 [73.8 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main arm64 libkrb5support0 arm64 1.18.3-4 [64.7 kB] Get:134 http://debian.oregonstate.edu/debian unstable/main arm64 libk5crypto3 arm64 1.18.3-4 [114 kB] Get:135 http://debian.oregonstate.edu/debian unstable/main arm64 libkeyutils1 arm64 1.6.1-2 [15.4 kB] Get:136 http://debian.oregonstate.edu/debian unstable/main arm64 libssl1.1 arm64 1.1.1k-1 [1386 kB] Get:137 http://debian.oregonstate.edu/debian unstable/main arm64 libkrb5-3 arm64 1.18.3-4 [346 kB] Get:138 http://debian.oregonstate.edu/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.18.3-4 [155 kB] Get:139 http://debian.oregonstate.edu/debian unstable/main arm64 libtirpc3 arm64 1.3.1-1 [80.0 kB] Get:140 http://debian.oregonstate.edu/debian unstable/main arm64 libnsl2 arm64 1.3.0-2 [36.9 kB] Get:141 http://debian.oregonstate.edu/debian unstable/main arm64 libtirpc-dev arm64 1.3.1-1 [192 kB] Get:142 http://debian.oregonstate.edu/debian unstable/main arm64 libnsl-dev arm64 1.3.0-2 [66.1 kB] Get:143 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.31-10 [2029 kB] Get:144 http://debian.oregonstate.edu/debian unstable/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get:145 http://debian.oregonstate.edu/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get:146 http://debian.oregonstate.edu/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.0.6-4 [255 kB] Get:147 http://debian.oregonstate.edu/debian unstable/main arm64 libjpeg-dev arm64 1:2.0.6-4 [67.8 kB] Get:148 http://debian.oregonstate.edu/debian unstable/main arm64 libhdf5-dev arm64 1.10.6+repack-2 [2543 kB] Get:149 http://debian.oregonstate.edu/debian unstable/main arm64 libsuperlu-dev arm64 5.2.2+dfsg1-2 [21.4 kB] Get:150 http://debian.oregonstate.edu/debian unstable/main arm64 libarmadillo-dev arm64 1:10.1.2+dfsg-5 [386 kB] Get:151 http://debian.oregonstate.edu/debian unstable/main arm64 libasan6 arm64 10.2.1-6 [2002 kB] Get:152 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 10.2.1-6 [9468 B] Get:153 http://debian.oregonstate.edu/debian unstable/main arm64 libbamtools2.5.1 arm64 2.5.1+dfsg-8 [142 kB] Get:154 http://debian.oregonstate.edu/debian unstable/main arm64 libbamtools-dev arm64 2.5.1+dfsg-8 [197 kB] Get:155 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 10.2.1-6 [91.6 kB] Get:156 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 10.2.1-6 [23.8 kB] Get:157 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 10.2.1-6 [794 kB] Get:158 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 10.2.1-6 [1957 kB] Get:159 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 10.2.1-6 [759 kB] Get:160 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-10-dev arm64 10.2.1-6 [876 kB] Get:161 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-10-dev arm64 10.2.1-6 [1704 kB] Get:162 http://debian.oregonstate.edu/debian unstable/main arm64 libboost1.74-dev arm64 1.74.0-9 [9534 kB] Get:163 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-math1.74.0 arm64 1.74.0-9 [490 kB] Get:164 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-math1.74-dev arm64 1.74.0-9 [581 kB] Get:165 http://debian.oregonstate.edu/debian unstable/main arm64 libboost-math-dev arm64 1.74.0.3 [4532 B] Get:166 http://debian.oregonstate.edu/debian unstable/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-2 [4284 B] Get:167 http://debian.oregonstate.edu/debian unstable/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-2 [4348 B] Get:168 http://debian.oregonstate.edu/debian unstable/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get:169 http://debian.oregonstate.edu/debian unstable/main arm64 libjsoncpp-dev arm64 1.9.4-4 [25.4 kB] Get:170 http://debian.oregonstate.edu/debian unstable/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-11 [32.8 kB] Get:171 http://debian.oregonstate.edu/debian unstable/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-11 [37.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 259 MB in 2s (113 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10482 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-7_amd64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../001-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../003-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package perl-modules-5.32. Preparing to unpack .../005-perl-modules-5.32_5.32.1-3_all.deb ... Unpacking perl-modules-5.32 (5.32.1-3) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../006-libperl5.32_5.32.1-3_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-3) ... Selecting previously unselected package perl. Preparing to unpack .../007-perl_5.32.1-3_amd64.deb ... Unpacking perl (5.32.1-3) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../008-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package gcc-10-base:arm64. Preparing to unpack .../009-gcc-10-base_10.2.1-6_arm64.deb ... Unpacking gcc-10-base:arm64 (10.2.1-6) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../010-libncurses6_6.2+20201114-2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../011-libprocps8_2%3a3.3.17-4_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-4) ... Selecting previously unselected package procps. Preparing to unpack .../012-procps_2%3a3.3.17-4_amd64.deb ... Unpacking procps (2:3.3.17-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../013-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../014-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../015-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../016-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../017-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../018-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../019-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../020-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../021-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../022-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../023-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../024-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package binutils-aarch64-linux-gnu. Preparing to unpack .../025-binutils-aarch64-linux-gnu_2.35.2-2_amd64.deb ... Unpacking binutils-aarch64-linux-gnu (2.35.2-2) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../026-libcrypt-dev_1%3a4.4.18-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.18-2) ... Selecting previously unselected package libtirpc-dev:amd64. Preparing to unpack .../027-libtirpc-dev_1.3.1-1_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.1-1) ... Selecting previously unselected package libnsl-dev:amd64. Preparing to unpack .../028-libnsl-dev_1.3.0-2_amd64.deb ... Unpacking libnsl-dev:amd64 (1.3.0-2) ... Selecting previously unselected package libc6-dev:amd64. Preparing to unpack .../029-libc6-dev_2.31-10_amd64.deb ... Unpacking libc6-dev:amd64 (2.31-10) ... Selecting previously unselected package libstdc++-10-dev:amd64. Preparing to unpack .../030-libstdc++-10-dev_10.2.1-6_amd64.deb ... Unpacking libstdc++-10-dev:amd64 (10.2.1-6) ... Selecting previously unselected package g++-10. Preparing to unpack .../031-g++-10_10.2.1-6_amd64.deb ... Unpacking g++-10 (10.2.1-6) ... Selecting previously unselected package g++. Preparing to unpack .../032-g++_4%3a10.2.1-1_amd64.deb ... Unpacking g++ (4:10.2.1-1) ... Selecting previously unselected package libdpkg-perl. Preparing to unpack .../033-libdpkg-perl_1.20.7.1_all.deb ... Unpacking libdpkg-perl (1.20.7.1) ... Selecting previously unselected package dpkg-dev. Preparing to unpack .../034-dpkg-dev_1.20.7.1_all.deb ... Unpacking dpkg-dev (1.20.7.1) ... Selecting previously unselected package build-essential. Preparing to unpack .../035-build-essential_12.9_amd64.deb ... Unpacking build-essential (12.9) ... Selecting previously unselected package cmake-data. Preparing to unpack .../036-cmake-data_3.18.4-2_all.deb ... Unpacking cmake-data (3.18.4-2) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../037-libicu67_67.1-6_amd64.deb ... Unpacking libicu67:amd64 (67.1-6) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../038-libxml2_2.9.10+dfsg-6.3+b1_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.3+b1) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../039-libarchive13_3.4.3-2+b1_amd64.deb ... Unpacking libarchive13:amd64 (3.4.3-2+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../040-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../041-libsasl2-modules-db_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../042-libsasl2-2_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../043-libldap-2.4-2_2.4.57+dfsg-2_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.57+dfsg-2) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../044-libnghttp2-14_1.43.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../045-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../046-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../047-libssh2-1_1.9.0-3_amd64.deb ... Unpacking libssh2-1:amd64 (1.9.0-3) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../048-libcurl4_7.74.0-1.1_amd64.deb ... 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Selecting previously unselected package sbuild-build-depends-main-dummy:arm64. Preparing to unpack .../170-sbuild-build-depends-main-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-1) ... Setting up libexpat1:amd64 (2.2.10-2) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up hdf5-helpers:arm64 (1.10.6+repack-2) ... Setting up libicu67:amd64 (67.1-6) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up perl-modules-5.32 (5.32.1-3) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up linux-libc-dev:arm64 (5.10.26-1) ... Setting up gettext-base (0.21-4) ... Setting up binutils-aarch64-linux-gnu (2.35.2-2) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up gcc-10-base:arm64 (10.2.1-6) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up cross-config (2.6.17) ... Setting up libtirpc-dev:amd64 (1.3.1-1) ... Setting up libuv1:amd64 (1.40.0-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libc6-arm64-cross (2.31-9cross4) ... Setting up autopoint (0.21-4) ... Setting up libperl5.32:amd64 (5.32.1-3) ... Setting up gcc-10-cross-base (10.2.1-6cross1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up linux-libc-dev-arm64-cross (5.10.13-1cross4) ... Setting up libjsoncpp24:amd64 (1.9.4-4) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up sensible-utils (0.0.14) ... Setting up librhash0:amd64 (1.4.1-2) ... Setting up libcrypt-dev:amd64 (1:4.4.18-2) ... Setting up libuchardet0:amd64 (0.0.7-1) ... 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Setting up libc6-dev-arm64-cross (2.31-9cross4) ... Setting up libstdc++6-arm64-cross (10.2.1-6cross1) ... Setting up perl (5.32.1-3) ... Setting up libitm1-arm64-cross (10.2.1-6cross1) ... Setting up ucf (3.0043) ... Setting up libdpkg-perl (1.20.7.1) ... Setting up autoconf (2.69-14) ... Setting up g++ (4:10.2.1-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-4) ... Setting up cpp-10-aarch64-linux-gnu (10.2.1-6cross1) ... Setting up libcurl4:amd64 (7.74.0-1.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-which-perl (1.23-1) ... Setting up libubsan1-arm64-cross (10.2.1-6cross1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libgcc-10-dev-arm64-cross (10.2.1-6cross1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up dpkg-dev (1.20.7.1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up dh-autoreconf (20) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up cpp-aarch64-linux-gnu (4:10.2.1-1) ... Setting up cmake (3.18.4-2) ... Setting up build-essential (12.9) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libstdc++-10-dev-arm64-cross (10.2.1-6cross1) ... Setting up gcc-10-aarch64-linux-gnu (10.2.1-6cross1) ... Setting up po-debconf (1.0.21+nmu1) ... 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++-10-aarch64-linux-gnu (10.2.1-6cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+b1) ... 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 dh-strip-nondeterminism (1.11.0-1) ... Setting up gcc-aarch64-linux-gnu (4:10.2.1-1) ... Setting up debhelper (13.3.4) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-aarch64-linux-gnu (4:10.2.1-1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up libdebian-dpkgcross-perl (2.6.17) ... Setting up dpkg-cross (2.6.17) ... Setting up crossbuild-essential-arm64 (12.9) ... Setting up libcrypt1:arm64 (1:4.4.18-2) ... Setting up libgcc-s1:arm64 (10.2.1-6) ... Setting up libc6:arm64 (2.31-10) ... Setting up libcrypt-dev:arm64 (1:4.4.18-2) ... Setting up libstdc++6:arm64 (10.2.1-6) ... Setting up liblsan0:arm64 (10.2.1-6) ... Setting up libitm1:arm64 (10.2.1-6) ... Setting up libtsan0:arm64 (10.2.1-6) ... Setting up libdisorder0:arm64 (0.0.2+git20130809.8062ee1-2) ... Setting up libkeyutils1:arm64 (1.6.1-2) ... Setting up libssl1.1:arm64 (1.1.1k-1) ... Setting up libsmithwaterman0:arm64 (0.0+git20160702.2610e25-11) ... Setting up zlib1g:arm64 (1:1.2.11.dfsg-2) ... Setting up libcom-err2:arm64 (1.46.2-1) ... Setting up libgomp1:arm64 (10.2.1-6) ... Setting up libaec0:arm64 (1.0.4-1) ... Setting up libasan6:arm64 (10.2.1-6) ... Setting up libkrb5support0:arm64 (1.18.3-4) ... Setting up libblas3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ... Setting up libbamtools2.5.1:arm64 (2.5.1+dfsg-8) ... Setting up libatomic1:arm64 (10.2.1-6) ... Setting up libk5crypto3:arm64 (1.18.3-4) ... Setting up libdisorder-dev:arm64 (0.0.2+git20130809.8062ee1-2) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up libjsoncpp24:arm64 (1.9.4-4) ... Setting up libboost-math1.74.0:arm64 (1.74.0-9) ... Setting up libubsan1:arm64 (10.2.1-6) ... Setting up libkrb5-3:arm64 (1.18.3-4) ... Setting up libblas-dev:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsz2:arm64 (1.0.4-1) ... Setting up libjsoncpp-dev:arm64 (1.9.4-4) ... Setting up liblapack3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libgcc-10-dev:arm64 (10.2.1-6) ... Setting up libaec-dev:arm64 (1.0.4-1) ... Setting up libarpack2:arm64 (3.8.0-1) ... Setting up libsuperlu5:arm64 (5.2.2+dfsg1-2) ... Setting up libbamtools-dev:arm64 (2.5.1+dfsg-8) ... Setting up liblapack-dev:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.18.3-4) ... Setting up libsmithwaterman-dev:arm64 (0.0+git20160702.2610e25-11) ... Setting up libhdf5-103-1:arm64 (1.10.6+repack-2) ... Setting up libhdf5-cpp-103-1:arm64 (1.10.6+repack-2) ... Setting up libsuperlu-dev:arm64 (5.2.2+dfsg1-2) ... Setting up libhdf5-hl-100:arm64 (1.10.6+repack-2) ... Setting up libtirpc3:arm64 (1.3.1-1) ... Setting up libarmadillo10:arm64 (1:10.1.2+dfsg-5) ... Setting up libarpack2-dev:arm64 (3.8.0-1) ... Setting up libhdf5-hl-cpp-100:arm64 (1.10.6+repack-2) ... Setting up libtirpc-dev:arm64 (1.3.1-1) ... Setting up libhdf5-fortran-102:arm64 (1.10.6+repack-2) ... Setting up libnsl2:arm64 (1.3.0-2) ... Setting up libhdf5-hl-fortran-100:arm64 (1.10.6+repack-2) ... Setting up libnsl-dev:arm64 (1.3.0-2) ... Setting up libc6-dev:arm64 (2.31-10) ... Setting up libstdc++-10-dev:arm64 (10.2.1-6) ... Setting up libboost1.74-dev:arm64 (1.74.0-9) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.0.6-4) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up libboost-math1.74-dev:arm64 (1.74.0-9) ... Setting up libboost-math-dev:arm64 (1.74.0.3) ... Setting up libjpeg-dev:arm64 (1:2.0.6-4) ... Setting up libhdf5-dev:arm64 (1.10.6+repack-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libarmadillo-dev:arm64 (1:10.1.2+dfsg-5) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.31-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-14-amd64 #1 SMP Debian 4.19.171-2 (2021-01-30) amd64 (x86_64) Toolchain package versions: binutils_2.35.2-2 dpkg-dev_1.20.7.1 g++-10_10.2.1-6 gcc-10_10.2.1-6 libc6-dev_2.31-10 libstdc++-10-dev_10.2.1-6 libstdc++-10-dev-arm64-cross_10.2.1-6cross1 libstdc++6_10.2.1-6 libstdc++6-arm64-cross_10.2.1-6cross1 linux-libc-dev_5.10.26-1 Package versions: adduser_3.118 apt_2.2.2 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11 base-passwd_3.5.49 bash_5.1-2+b1 binutils_2.35.2-2 binutils-aarch64-linux-gnu_2.35.2-2 binutils-common_2.35.2-2 binutils-x86-64-linux-gnu_2.35.2-2 bsdextrautils_2.36.1-7 bsdutils_1:2.36.1-7 build-essential_12.9 bzip2_1.0.8-4 cmake_3.18.4-2 cmake-data_3.18.4-2 coreutils_8.32-4+b1 cpp_4:10.2.1-1 cpp-10_10.2.1-6 cpp-10-aarch64-linux-gnu_10.2.1-6cross1 cpp-8_8.4.0-7 cpp-aarch64-linux-gnu_4:10.2.1-1 cross-config_2.6.17 crossbuild-essential-arm64_12.9 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.76 debhelper_13.3.4 debian-archive-keyring_2021.1.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dpkg_1.20.7.1 dpkg-cross_2.6.17 dpkg-dev_1.20.7.1 dwz_0.14-1 e2fsprogs_1.46.2-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-7 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1 g++-10_10.2.1-6 g++-10-aarch64-linux-gnu_10.2.1-6cross1 g++-aarch64-linux-gnu_4:10.2.1-1 gcc_4:10.2.1-1 gcc-10_10.2.1-6 gcc-10-aarch64-linux-gnu_10.2.1-6cross1 gcc-10-aarch64-linux-gnu-base_10.2.1-6cross1 gcc-10-base_10.2.1-6 gcc-10-cross-base_10.2.1-6cross1 gcc-8-base_8.4.0-7 gcc-9-base_9.3.0-22 gcc-aarch64-linux-gnu_4:10.2.1-1 gettext_0.21-4 gettext-base_0.21-4 gpgv_2.2.27-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.2.2 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2+b1 libarmadillo-dev_1:10.1.2+dfsg-5 libarmadillo10_1:10.1.2+dfsg-5 libarpack2_3.8.0-1 libarpack2-dev_3.8.0-1 libasan5_9.3.0-22 libasan6_10.2.1-6 libasan6-arm64-cross_10.2.1-6cross1 libatomic1_10.2.1-6 libatomic1-arm64-cross_10.2.1-6cross1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbamtools-dev_2.5.1+dfsg-8 libbamtools2.5.1_2.5.1+dfsg-8 libbinutils_2.35.2-2 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36.1-7 libboost-math-dev_1.74.0.3 libboost-math1.74-dev_1.74.0-9 libboost-math1.74.0_1.74.0-9 libboost1.74-dev_1.74.0-9 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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----- 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05:51:37 2020 UTC gpgv: using RSA key 90E2D2C1AD146A1B7EBB891DBBC17EBB1396F2F7 gpgv: issuer "stuart@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./tvc_5.0.3+git20151221.80e144e+dfsg-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.arm64 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-5112abf9-b26a-4c97-9e97-be98462e60b5 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarm64 -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 aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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-aarch64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=aarch64 -DCMAKE_C_COMPILER=aarch64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=aarch64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/aarch64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/aarch64-linux-gnu-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/aarch64-linux-gnu-qmake -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler 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/<>/VariantCaller/TargetsManager.cpp [ 9%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-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 [ 10%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /<>/external/vcflib/split.cpp [ 14%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<>/external/vcflib/tabixpp/tabix.cpp [ 15%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/aarch64-linux-gnu-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 -ffile-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 /<>/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’: /<>/external/vcflib/tabixpp/index.c:336:35: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 17%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /<>/obj-aarch64-linux-gnu/IonVersion.cpp [ 20%] Linking CXX executable tvcutils /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1 /usr/bin/aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 20%] Built target tvcutils make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= Dependee "/<>/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake" is newer than depender "/<>/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/depend.internal". Dependee "/<>/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/depend.internal". Scanning dependencies of target tvcassembly make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 21%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-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 [ 28%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu/include/string.h:495, from /usr/aarch64-linux-gnu/include/c++/10/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/aarch64-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long 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/aarch64-linux-gnu-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -c /<>/obj-aarch64-linux-gnu/IonVersion.cpp [ 31%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/aarch64-linux-gnu-g++ -g -O2 -ffile-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-aarch64-linux-gnu' [ 31%] Built target tvcassembly make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= Dependee "/<>/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake" is newer than depender "/<>/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/depend.internal". Dependee "/<>/obj-aarch64-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/depend.internal". Scanning dependencies of target tvc make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-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:349, 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:349, 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:349, 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:349, 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/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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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[-Wdeprecated-declarations] 240 | Json::Reader recal_reader; | ^~~~~~~~~~~~ In file included from /usr/include/jsoncpp/json/json.h:11, from /<>/Calibration/CalibrationHelper.h:23, from /<>/Calibration/LinearCalibrationModel.h:16, from /<>/VariantCaller/Bookkeeping/InputStructures.h:19, from /<>/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/include/jsoncpp/json/reader.h:37:63: note: declared here 37 | "Use CharReader and CharReaderBuilder instead.") JSON_API Reader { | ^~~~~~ /<>/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: ‘Json::Reader::Reader()’ is deprecated: Use CharReader and CharReaderBuilder instead [-Wdeprecated-declarations] 240 | Json::Reader recal_reader; | ^~~~~~~~~~~~ In file included from /usr/include/jsoncpp/json/json.h:11, from /<>/Calibration/CalibrationHelper.h:23, from /<>/Calibration/LinearCalibrationModel.h:16, from /<>/VariantCaller/Bookkeeping/InputStructures.h:19, from /<>/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/include/jsoncpp/json/reader.h:56:3: note: declared here 56 | Reader(); | ^~~~~~ [ 50%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o /usr/bin/aarch64-linux-gnu-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 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-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -c /<>/external/vcflib/Variant.cpp [ 78%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /<>/external/vcflib/split.cpp [ 79%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-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 /<>/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’: /<>/external/vcflib/tabixpp/index.c:336:35: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 82%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-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 /<>/Calibration/LinearCalibrationModel.cpp: In member function ‘void LinearCalibrationModel::SaveModelFileToBamComments(std::vector >&, const string&) const’: /<>/Calibration/LinearCalibrationModel.cpp:708:20: warning: ‘FastWriter’ is deprecated: Use StreamWriterBuilder instead [-Wdeprecated-declarations] 708 | Json::FastWriter writer; | ^~~~~~ In file included from /usr/include/jsoncpp/json/json.h:13, from /<>/Calibration/CalibrationHelper.h:23, from /<>/Calibration/LinearCalibrationModel.h:16, from /<>/Calibration/LinearCalibrationModel.cpp:13: /usr/include/jsoncpp/json/writer.h:168:70: note: declared here 168 | class JSONCPP_DEPRECATED("Use StreamWriterBuilder instead") JSON_API FastWriter | ^~~~~~~~~~ [ 90%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-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/aarch64-linux-gnu-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 -ffile-prefix-map=/<>=. -fstack-protector-strong 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-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/file-io/ion_util.c.o -c /<>/file-io/ion_util.c [ 96%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o /usr/bin/aarch64-linux-gnu-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/file-io/ion_error.c.o -c /<>/file-io/ion_error.c [ 98%] Building CXX object CMakeFiles/tvc.dir/IonVersion.cpp.o /usr/bin/aarch64-linux-gnu-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/IonVersion.cpp.o -c /<>/obj-aarch64-linux-gnu/IonVersion.cpp [100%] Linking CXX executable tvc /usr/bin/cmake -E 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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 CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o 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-aarch64-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start 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/<>/obj-aarch64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 20%] Built target tvcutils make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 31%] Built target tvcassembly make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tvc/usr/bin/tvc -- Installing: /<>/debian/tvc/usr/bin/tvcassembly -- Installing: /<>/debian/tvc/usr/bin/tvcutils -- Installing: /<>/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-aarch64-linux-gnu' dh_installdocs -a dh_installchangelogs -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc 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_arm64.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.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 2021-03-29T09:20:42Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.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: arm64 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). Checksums-Sha1: aa54634805ba2f06bdfc28d4e02776386165b52f 10451020 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb d0d1b5e7788dd023e655bf6c5a3b89dcd186b426 6984 tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.buildinfo 4bbe20f431621165e56bdb7d3279f3b896b464b9 996320 tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb Checksums-Sha256: 7a1b69432e15216b39c679764717b39925f7e7df9f781dc81093244273c66c66 10451020 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb 6f19e0a4f198c5b1e616cd1c4ce5833729601956a9fe29483e91c424119cddfa 6984 tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.buildinfo 176fd7c8033c66cbe2c525d9fd41f3fcb02daa7d8d6d9440abb27142643c153f 996320 tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb Files: f03e364cb9a90d878a01b5ece73fb35d 10451020 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb 98326e934f4a8a62e8a1df1201541264 6984 science optional tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.buildinfo b77e3355b418231f2d62e3cea83b94d0 996320 science optional tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: tvc Binary: tvc tvc-dbgsym Architecture: arm64 Version: 5.0.3+git20151221.80e144e+dfsg-3 Checksums-Md5: f03e364cb9a90d878a01b5ece73fb35d 10451020 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb b77e3355b418231f2d62e3cea83b94d0 996320 tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb Checksums-Sha1: aa54634805ba2f06bdfc28d4e02776386165b52f 10451020 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb 4bbe20f431621165e56bdb7d3279f3b896b464b9 996320 tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb Checksums-Sha256: 7a1b69432e15216b39c679764717b39925f7e7df9f781dc81093244273c66c66 10451020 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb 176fd7c8033c66cbe2c525d9fd41f3fcb02daa7d8d6d9440abb27142643c153f 996320 tvc_5.0.3+git20151221.80e144e+dfsg-3_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 29 Mar 2021 09:20:41 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-14), automake (= 1:1.16.3-2), autopoint (= 0.21-4), autotools-dev (= 20180224.1+nmu1), base-files (= 11), base-passwd (= 3.5.49), bash (= 5.1-2+b1), binutils (= 2.35.2-2), binutils-common (= 2.35.2-2), binutils-x86-64-linux-gnu (= 2.35.2-2), bsdextrautils (= 2.36.1-7), bsdutils (= 1:2.36.1-7), build-essential (= 12.9), bzip2 (= 1.0.8-4), cmake (= 3.18.4-2), cmake-data (= 3.18.4-2), coreutils (= 8.32-4+b1), cpp (= 4:10.2.1-1), cpp-10 (= 10.2.1-6), dash (= 0.5.11+git20210120+802ebd4-1), debconf (= 1.5.76), debhelper (= 13.3.4), debianutils (= 4.11.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.11.0-1), diffutils (= 1:3.7-5), dpkg (= 1.20.7.1), dpkg-dev (= 1.20.7.1), dwz (= 0.14-1), file (= 1:5.39-3), findutils (= 4.8.0-1), g++ (= 4:10.2.1-1), g++-10 (= 10.2.1-6), gcc (= 4:10.2.1-1), gcc-10 (= 10.2.1-6), gcc-10-base (= 10.2.1-6), gettext (= 0.21-4), gettext-base (= 0.21-4), grep (= 3.6-1), groff-base (= 1.22.4-6), gzip (= 1.10-4), hdf5-helpers (= 1.10.6+repack-2), hostname (= 3.23), init-system-helpers (= 1.60), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10), libaec-dev (= 1.0.4-1), libaec0 (= 1.0.4-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.4.3-2+b1), libarmadillo-dev (= 1:10.1.2+dfsg-5), libarmadillo10 (= 1:10.1.2+dfsg-5), libarpack2 (= 3.8.0-1), libarpack2-dev (= 3.8.0-1), libasan6 (= 10.2.1-6), libatomic1 (= 10.2.1-6), libattr1 (= 1:2.4.48-6), libaudit-common (= 1:3.0-2), libaudit1 (= 1:3.0-2), libbamtools-dev (= 2.5.1+dfsg-8), libbamtools2.5.1 (= 2.5.1+dfsg-8), libbinutils (= 2.35.2-2), libblas-dev (= 3.9.0-3), libblas3 (= 3.9.0-3), libblkid1 (= 2.36.1-7), libboost-math-dev (= 1.74.0.3), libboost-math1.74-dev (= 1.74.0-9), libboost-math1.74.0 (= 1.74.0-9), libboost1.74-dev (= 1.74.0-9), libbrotli1 (= 1.0.9-2+b2), libbz2-1.0 (= 1.0.8-4), libc-bin (= 2.31-10), libc-dev-bin (= 2.31-10), libc6 (= 2.31-10), libc6-dev (= 2.31-10), libcap-ng0 (= 0.7.9-2.2+b1), libcc1-0 (= 10.2.1-6), libcom-err2 (= 1.46.2-1), libcrypt-dev (= 1:4.4.18-2), libcrypt1 (= 1:4.4.18-2), libctf-nobfd0 (= 2.35.2-2), libctf0 (= 2.35.2-2), libcurl4 (= 7.74.0-1.1), libdb5.3 (= 5.3.28+dfsg1-0.8), libdebconfclient0 (= 0.257), libdebhelper-perl (= 13.3.4), libdisorder-dev (= 0.0.2+git20130809.8062ee1-2), libdisorder0 (= 0.0.2+git20130809.8062ee1-2), libdpkg-perl (= 1.20.7.1), libelf1 (= 0.183-3), libexpat1 (= 2.2.10-2), libffi7 (= 3.3-6), libfile-stripnondeterminism-perl (= 1.11.0-1), libgcc-10-dev (= 10.2.1-6), libgcc-s1 (= 10.2.1-6), libgcrypt20 (= 1.8.7-3), libgdbm-compat4 (= 1.19-2), libgdbm6 (= 1.19-2), libgfortran5 (= 10.2.1-6), libgmp10 (= 2:6.2.1+dfsg-1), libgnutls30 (= 3.7.1-1), libgomp1 (= 10.2.1-6), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.18.3-4), libhdf5-103-1 (= 1.10.6+repack-2), libhdf5-cpp-103-1 (= 1.10.6+repack-2), libhdf5-dev (= 1.10.6+repack-2), libhdf5-fortran-102 (= 1.10.6+repack-2), libhdf5-hl-100 (= 1.10.6+repack-2), libhdf5-hl-cpp-100 (= 1.10.6+repack-2), libhdf5-hl-fortran-100 (= 1.10.6+repack-2), libhogweed6 (= 3.7-2.1), libicu67 (= 67.1-6), libidn2-0 (= 2.3.0-5), libisl23 (= 0.23-1), libitm1 (= 10.2.1-6), libjpeg-dev (= 1:2.0.6-4), libjpeg62-turbo (= 1:2.0.6-4), libjpeg62-turbo-dev (= 1:2.0.6-4), libjsoncpp-dev (= 1.9.4-4), libjsoncpp24 (= 1.9.4-4), libk5crypto3 (= 1.18.3-4), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.18.3-4), libkrb5support0 (= 1.18.3-4), liblapack-dev (= 3.9.0-3), liblapack3 (= 3.9.0-3), libldap-2.4-2 (= 2.4.57+dfsg-2), liblsan0 (= 10.2.1-6), liblz4-1 (= 1.9.3-1), liblzma5 (= 5.2.5-2), libmagic-mgc (= 1:5.39-3), libmagic1 (= 1:5.39-3), libmount1 (= 2.36.1-7), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.2+20201114-2), libncursesw6 (= 6.2+20201114-2), libnettle8 (= 3.7-2.1), libnghttp2-14 (= 1.43.0-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libp11-kit0 (= 0.23.22-1), libpam-modules (= 1.4.0-7), libpam-modules-bin (= 1.4.0-7), libpam-runtime (= 1.4.0-7), libpam0g (= 1.4.0-7), libpcre2-8-0 (= 10.36-2), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.1-3), libpipeline1 (= 1.5.3-1), libprocps8 (= 2:3.3.17-4), libpsl5 (= 0.21.0-1.2), libquadmath0 (= 10.2.1-6), librhash0 (= 1.4.1-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.27+dfsg-2.1), libsasl2-modules-db (= 2.1.27+dfsg-2.1), libseccomp2 (= 2.5.1-1), libselinux1 (= 3.1-3), libsigsegv2 (= 2.13-1), libsmartcols1 (= 2.36.1-7), libsmithwaterman-dev (= 0.0+git20160702.2610e25-11), libsmithwaterman0 (= 0.0+git20160702.2610e25-11), libssh2-1 (= 1.9.0-3), libssl1.1 (= 1.1.1k-1), libstdc++-10-dev (= 10.2.1-6), libstdc++6 (= 10.2.1-6), libsub-override-perl (= 0.09-2), libsuperlu-dev (= 5.2.2+dfsg1-2), libsuperlu5 (= 5.2.2+dfsg1-2), libsystemd0 (= 247.3-3), libsz2 (= 1.0.4-1), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2+20201114-2), libtirpc-common (= 1.3.1-1), libtirpc-dev (= 1.3.1-1), libtirpc3 (= 1.3.1-1), libtool (= 2.4.6-15), libtsan0 (= 10.2.1-6), libubsan1 (= 10.2.1-6), libuchardet0 (= 0.0.7-1), libudev1 (= 247.3-3), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36.1-7), libuv1 (= 1.40.0-1), libxml2 (= 2.9.10+dfsg-6.3+b1), libzstd1 (= 1.4.8+dfsg-2.1), linux-libc-dev (= 5.10.26-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-5), make (= 4.3-4), man-db (= 2.9.4-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2+20201114-2), ncurses-bin (= 6.2+20201114-2), patch (= 2.7.6-7), perl (= 5.32.1-3), perl-base (= 5.32.1-3), perl-modules-5.32 (= 5.32.1-3), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-4), sed (= 4.7-1), sensible-utils (= 0.0.14), sysvinit-utils (= 2.96-6), tar (= 1.34+dfsg-1), util-linux (= 2.36.1-7), xz-utils (= 5.2.5-2), 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_arm64.deb ----------------------------------------------------- new Debian package, version 2.0. size 10451020 bytes: control archive=704 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: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 10596 Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-3) Section: debug Priority: optional Description: debug symbols for tvc Build-Ids: 0c4b9c45fa32e63f7488140507829ed9bf581846 305aa5841787ee9a74b67e600f81b9b5addbd3c1 b559ad2bc774ab502d833bb9711e032f6440fe74 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/0c/ -rw-r--r-- root/root 7272672 2020-03-01 04:57 ./usr/lib/debug/.build-id/0c/4b9c45fa32e63f7488140507829ed9bf581846.debug drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/30/ -rw-r--r-- root/root 770024 2020-03-01 04:57 ./usr/lib/debug/.build-id/30/5aa5841787ee9a74b67e600f81b9b5addbd3c1.debug drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/b5/ -rw-r--r-- root/root 2344376 2020-03-01 04:57 ./usr/lib/debug/.build-id/b5/59ad2bc774ab502d833bb9711e032f6440fe74.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/aarch64-linux-gnu/ -rw-r--r-- root/root 446504 2020-03-01 04:57 ./usr/lib/debug/.dwz/aarch64-linux-gnu/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_arm64.deb ---------------------------------------------- new Debian package, version 2.0. size 996320 bytes: control archive=1680 bytes. 993 bytes, 16 lines control 2459 bytes, 28 lines md5sums Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-3 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 3149 Depends: libarmadillo10 (>= 1:10.1.2+dfsg), libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.29), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 4.5), libjsoncpp24 (>= 1.9.4), 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 1021664 2020-03-01 04:57 ./usr/bin/tvc -rwxr-xr-x root/root 192008 2020-03-01 04:57 ./usr/bin/tvcassembly -rwxr-xr-x root/root 561288 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 (91.6 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 libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libproc-processtable-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils readline-common t1utils unzip Suggested packages: libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libpackage-stash-xs-perl libref-util-perl libtype-tiny-xs-perl The following NEW packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libproc-processtable-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils readline-common sbuild-build-depends-lintian-dummy:arm64 t1utils unzip 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 7626 kB of archives. After this operation, 21.7 MB of additional disk space will be used. 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libpackage-stash-perl all 0.39-1 [21.9 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b3 [12.0 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1+b1 [13.8 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.118-1 [53.5 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-gzip-perl amd64 0.19-1+b7 [17.4 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libproc-processtable-perl amd64 0.59-2+b1 [45.9 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.018+ds-1+b1 [99.3 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.018+ds-1+b1 [103 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-4+b8 [8724 B] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.12-1+b1 [13.0 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.8-1+b1 [197 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-moment-perl amd64 0.44-1+b3 [75.8 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.012001-2 [351 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b2 [20.3 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 5.08-1 [90.6 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.82+repack-1+b1 [35.8 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 lzip amd64 1.22-3 [88.5 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 unzip amd64 6.0-26 [171 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.104.0 [1265 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7626 kB in 0s (25.7 MB/s) Selecting previously unselected package readline-common. (Reading database ... 40136 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package diffstat. Preparing to unpack .../02-diffstat_1.64-1_amd64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../03-libassuan0_2.5.4-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.4-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../04-gpgconf_2.2.27-1_amd64.deb ... Unpacking gpgconf (2.2.27-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../05-libsqlite3-0_3.34.1-3_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.34.1-3) ... Selecting previously unselected package gpg. 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Setting up libtext-levenshteinxs-perl (0.03-4+b8) ... Setting up libperlio-gzip-perl (0.19-1+b7) ... Setting up readline-common (8.1-1) ... Setting up libhtml-html5-entities-perl (0.004-1.1) ... Setting up libsereal-decoder-perl (4.018+ds-1+b1) ... Setting up libmarkdown2:amd64 (2.2.6-1) ... Setting up liburi-perl (5.08-1) ... Setting up libemail-address-xs-perl (1.04-1+b3) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libtype-tiny-perl (1.012001-2) ... Setting up libtext-markdown-discount-perl:amd64 (0.12-1+b1) ... Setting up libexception-class-perl (1.44-1) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up libdata-optlist-perl (0.110-1.1) ... Setting up gpgconf (2.2.27-1) ... Setting up gpg (2.2.27-1) ... Setting up libsub-exporter-perl (0.987-1) ... Setting up libiterator-perl (0.03+ds1-1.1) ... Setting up libiterator-util-perl (0.02+ds1-1.1) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libpackage-stash-perl (0.39-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.004004-1) ... Setting up libmoox-aliases-perl (0.001006-1.1) ... Setting up libb-hooks-endofscope-perl (0.24-1.1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.104.0) ... Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ... Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.31-10) ... 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: 202728 Build-Time: 243 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 44 Job: tvc_5.0.3+git20151221.80e144e+dfsg-3 Lintian: pass Machine Architecture: amd64 Package: tvc Package-Time: 298 Source-Version: 5.0.3+git20151221.80e144e+dfsg-3 Space: 202728 Status: successful Version: 5.0.3+git20151221.80e144e+dfsg-3 -------------------------------------------------------------------------------- Finished at 2021-03-29T09:20:42Z Build needed 00:04:58, 202728k disk space