sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir +==============================================================================+ | tvc 5.0.3+git20151221.80e144e+dfsg-3 (i386) Sun, 27 Jun 2021 05:29:39 +0000 | +==============================================================================+ Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-3 Source Version: 5.0.3+git20151221.80e144e+dfsg-3 Distribution: unstable Machine Architecture: arm64 Host Architecture: i386 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-cbb58e6a-e1b0-4f47-9901-14d2e2dcc4bd' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-zCrs19/resolver-BeBgNW' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [161 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:4 http://mirror.einval.org/debian sid/main i386 Packages [8569 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9150 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8516 kB] Fetched 26.4 MB in 7s (3794 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://mirror.einval.org/debian sid/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (dsc) [2200 B] Get:2 http://mirror.einval.org/debian sid/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (tar) [745 kB] Get:3 http://mirror.einval.org/debian sid/main tvc 5.0.3+git20151221.80e144e+dfsg-3 (diff) [8968 B] Fetched 756 kB in 0s (13.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/tvc-zCrs19/tvc-5.0.3+git20151221.80e144e+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-zCrs19' 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:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 Filtered Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 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 [444 B] Get:5 copy:/<>/apt_archive ./ Packages [534 B] Fetched 1935 B in 0s (46.5 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-i686-linux-gnu bsdextrautils cmake cmake-data cpp-10-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-10-i686-linux-gnu g++-i686-linux-gnu gcc-10-base:i386 gcc-10-cross-base gcc-10-i686-linux-gnu gcc-10-i686-linux-gnu-base gcc-i686-linux-gnu gettext gettext-base groff-base hdf5-helpers:i386 intltool-debian libaec-dev:i386 libaec0:i386 libarchive-zip-perl libarchive13 libarmadillo-dev:i386 libarmadillo10:i386 libarpack2:i386 libarpack2-dev:i386 libasan6:i386 libasan6-i386-cross libatomic1:i386 libatomic1-i386-cross libbamtools-dev:i386 libbamtools2.5.1:i386 libblas-dev:i386 libblas3:i386 libboost-math-dev:i386 libboost-math1.74-dev:i386 libboost-math1.74.0:i386 libboost1.74-dev:i386 libbrotli1 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcom-err2:i386 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdisorder-dev:i386 libdisorder0:i386 libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:i386 libgcc-10-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgfortran5:i386 libgomp1:i386 libgomp1-i386-cross libgssapi-krb5-2:i386 libhdf5-103-1:i386 libhdf5-cpp-103-1:i386 libhdf5-dev:i386 libhdf5-fortran-102:i386 libhdf5-hl-100:i386 libhdf5-hl-cpp-100:i386 libhdf5-hl-fortran-100:i386 libicu67 libio-string-perl libitm1:i386 libitm1-i386-cross libjpeg-dev:i386 libjpeg62-turbo:i386 libjpeg62-turbo-dev:i386 libjsoncpp-dev:i386 libjsoncpp24 libjsoncpp24:i386 libk5crypto3:i386 libkeyutils1:i386 libkrb5-3:i386 libkrb5support0:i386 liblapack-dev:i386 liblapack3:i386 libldap-2.4-2 liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libncursesw6 libnghttp2-14 libnsl-dev:i386 libnsl2:i386 libpipeline1 libprocps8 libpsl5 libquadmath0:i386 libquadmath0-i386-cross librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:i386 libsmithwaterman0:i386 libssh2-1 libssl1.1:i386 libstdc++-10-dev:i386 libstdc++-10-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsub-override-perl libsuperlu-dev:i386 libsuperlu5:i386 libsz2:i386 libtirpc-dev:i386 libtirpc3:i386 libtool libubsan1:i386 libubsan1-i386-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:i386 linux-libc-dev-i386-cross m4 man-db po-debconf procps sensible-utils ucf zlib1g:i386 zlib1g-dev:i386 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc ninja-build gcc-10-locales cpp-doc dh-make binutils-multiarch g++-10-multilib-i686-linux-gnu gcc-10-doc gcc-10-multilib-i686-linux-gnu manpages-dev flex bison gdb-i686-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libitpp-dev:i386 libbamtools-doc:i386 liblapack-doc:i386 libboost1.74-doc:i386 libboost-atomic1.74-dev:i386 libboost-chrono1.74-dev:i386 libboost-container1.74-dev:i386 libboost-context1.74-dev:i386 libboost-contract1.74-dev:i386 libboost-coroutine1.74-dev:i386 libboost-date-time1.74-dev:i386 libboost-exception1.74-dev:i386 libboost-fiber1.74-dev:i386 libboost-filesystem1.74-dev:i386 libboost-graph1.74-dev:i386 libboost-graph-parallel1.74-dev:i386 libboost-iostreams1.74-dev:i386 libboost-locale1.74-dev:i386 libboost-log1.74-dev:i386 libboost-mpi1.74-dev:i386 libboost-mpi-python1.74-dev:i386 libboost-numpy1.74-dev:i386 libboost-program-options1.74-dev:i386 libboost-python1.74-dev:i386 libboost-random1.74-dev:i386 libboost-regex1.74-dev:i386 libboost-serialization1.74-dev:i386 libboost-stacktrace1.74-dev:i386 libboost-system1.74-dev:i386 libboost-test1.74-dev:i386 libboost-thread1.74-dev:i386 libboost-timer1.74-dev:i386 libboost-type-erasure1.74-dev:i386 libboost-wave1.74-dev:i386 libboost1.74-tools-dev:i386 libmpfrc++-dev:i386 libntl-dev:i386 libboost-nowide1.74-dev:i386 glibc-doc:i386 libc-l10n:i386 locales:i386 manpages-dev:i386 krb5-doc:i386 krb5-user:i386 libhdf5-doc:i386 libstdc++-10-doc:i386 libsuperlu-doc:i386 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:i386 libnss-nis:i386 libnss-nisplus:i386 ca-certificates libarchive-cpio-perl krb5-locales:i386 libldap-common libgpm2 publicsuffix libsasl2-modules libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bsdextrautils cmake cmake-data cpp-10-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-10-i686-linux-gnu g++-i686-linux-gnu gcc-10-base:i386 gcc-10-cross-base gcc-10-i686-linux-gnu gcc-10-i686-linux-gnu-base gcc-i686-linux-gnu gettext gettext-base groff-base hdf5-helpers:i386 intltool-debian libaec-dev:i386 libaec0:i386 libarchive-zip-perl libarchive13 libarmadillo-dev:i386 libarmadillo10:i386 libarpack2:i386 libarpack2-dev:i386 libasan6:i386 libasan6-i386-cross libatomic1:i386 libatomic1-i386-cross libbamtools-dev:i386 libbamtools2.5.1:i386 libblas-dev:i386 libblas3:i386 libboost-math-dev:i386 libboost-math1.74-dev:i386 libboost-math1.74.0:i386 libboost1.74-dev:i386 libbrotli1 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcom-err2:i386 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdisorder-dev:i386 libdisorder0:i386 libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:i386 libgcc-10-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgfortran5:i386 libgomp1:i386 libgomp1-i386-cross libgssapi-krb5-2:i386 libhdf5-103-1:i386 libhdf5-cpp-103-1:i386 libhdf5-dev:i386 libhdf5-fortran-102:i386 libhdf5-hl-100:i386 libhdf5-hl-cpp-100:i386 libhdf5-hl-fortran-100:i386 libicu67 libio-string-perl libitm1:i386 libitm1-i386-cross libjpeg-dev:i386 libjpeg62-turbo:i386 libjpeg62-turbo-dev:i386 libjsoncpp-dev:i386 libjsoncpp24 libjsoncpp24:i386 libk5crypto3:i386 libkeyutils1:i386 libkrb5-3:i386 libkrb5support0:i386 liblapack-dev:i386 liblapack3:i386 libldap-2.4-2 liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libncursesw6 libnghttp2-14 libnsl-dev:i386 libnsl2:i386 libpipeline1 libprocps8 libpsl5 libquadmath0:i386 libquadmath0-i386-cross librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsmithwaterman-dev:i386 libsmithwaterman0:i386 libssh2-1 libssl1.1:i386 libstdc++-10-dev:i386 libstdc++-10-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsub-override-perl libsuperlu-dev:i386 libsuperlu5:i386 libsz2:i386 libtirpc-dev:i386 libtirpc3:i386 libtool libubsan1:i386 libubsan1-i386-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:i386 linux-libc-dev-i386-cross m4 man-db po-debconf procps sbuild-build-depends-main-dummy:i386 sensible-utils ucf zlib1g:i386 zlib1g-dev:i386 0 upgraded, 157 newly installed, 0 to remove and 0 not upgraded. Need to get 232 MB of archives. After this operation, 1152 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://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get:8 http://mirror.einval.org/debian sid/main i386 gcc-10-base i386 10.2.1-6 [201 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libncursesw6 arm64 6.2+20201114-2 [121 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.39-3 [69.1 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-4 [173 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.69-14 [313 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.3-2 [814 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-4 [510 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 cmake-data all 3.18.4-2 [1725 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-6 [8468 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libarchive13 arm64 3.4.3-2+b1 [320 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 libssh2-1 arm64 1.9.0-3 [162 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libcurl4 arm64 7.74.0-1.3 [320 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 librhash0 arm64 1.4.1-2 [127 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libuv1 arm64 1.40.0-1 [126 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 cmake arm64 3.18.4-2 [3673 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 gcc-10-i686-linux-gnu-base arm64 10.2.1-6cross1 [202 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 cpp-10-i686-linux-gnu arm64 10.2.1-6cross1 [46.1 MB] Get:45 http://mirror.einval.org/debian sid/main arm64 cpp-i686-linux-gnu arm64 4:10.2.1-1 [16.8 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu1 [31.5 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 binutils-i686-linux-gnu arm64 2.35.2-2 [1967 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 gcc-10-cross-base all 10.2.1-6cross1 [197 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libc6-i386-cross all 2.31-9cross4 [1502 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-i386-cross all 10.2.1-6cross1 [49.7 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libgomp1-i386-cross all 10.2.1-6cross1 [104 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libitm1-i386-cross all 10.2.1-6cross1 [28.3 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 libatomic1-i386-cross all 10.2.1-6cross1 [9376 B] Get:54 http://mirror.einval.org/debian sid/main arm64 libasan6-i386-cross all 10.2.1-6cross1 [1923 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libstdc++6-i386-cross all 10.2.1-6cross1 [487 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libubsan1-i386-cross all 10.2.1-6cross1 [751 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libquadmath0-i386-cross all 10.2.1-6cross1 [228 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 libgcc-10-dev-i386-cross all 10.2.1-6cross1 [2323 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 gcc-10-i686-linux-gnu arm64 10.2.1-6cross1 [52.2 MB] Get:60 http://mirror.einval.org/debian sid/main arm64 gcc-i686-linux-gnu arm64 4:10.2.1-1 [1452 B] Get:61 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-i386-cross all 5.10.13-1cross4 [1396 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libc6-dev-i386-cross all 2.31-9cross4 [2224 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libstdc++-10-dev-i386-cross all 10.2.1-6cross1 [1775 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 g++-10-i686-linux-gnu arm64 10.2.1-6cross1 [49.2 MB] Get:65 http://mirror.einval.org/debian sid/main arm64 g++-i686-linux-gnu arm64 4:10.2.1-1 [1176 B] Get:66 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu1 [30.5 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu1 [41.6 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-i386 all 12.9 [6704 B] Get:80 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.6-15 [513 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.183-3 [164 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-4 [1261 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.3.4 [1049 kB] Get:93 http://mirror.einval.org/debian sid/main i386 hdf5-helpers i386 1.10.6+repack-4 [40.4 kB] Get:94 http://mirror.einval.org/debian sid/main i386 libgcc-s1 i386 10.2.1-6 [49.6 kB] Get:95 http://mirror.einval.org/debian sid/main i386 libcrypt1 i386 1:4.4.18-4 [97.2 kB] Get:96 http://mirror.einval.org/debian sid/main i386 libc6 i386 2.31-12 [2756 kB] Get:97 http://mirror.einval.org/debian sid/main i386 libaec0 i386 1.0.4-3 [21.3 kB] Get:98 http://mirror.einval.org/debian sid/main i386 libsz2 i386 1.0.4-3 [7064 B] Get:99 http://mirror.einval.org/debian sid/main i386 libaec-dev i386 1.0.4-3 [19.8 kB] Get:100 http://mirror.einval.org/debian sid/main i386 libblas3 i386 3.9.0-3 [147 kB] Get:101 http://mirror.einval.org/debian sid/main i386 libquadmath0 i386 10.2.1-6 [228 kB] Get:102 http://mirror.einval.org/debian sid/main i386 libgfortran5 i386 10.2.1-6 [643 kB] Get:103 http://mirror.einval.org/debian sid/main i386 liblapack3 i386 3.9.0-3 [1960 kB] Get:104 http://mirror.einval.org/debian sid/main i386 libarpack2 i386 3.8.0-1 [103 kB] Get:105 http://mirror.einval.org/debian sid/main i386 libstdc++6 i386 10.2.1-6 [527 kB] Get:106 http://mirror.einval.org/debian sid/main i386 libsuperlu5 i386 5.2.2+dfsg1-2 [161 kB] Get:107 http://mirror.einval.org/debian sid/main i386 libarmadillo10 i386 1:10.1.2+dfsg-6 [103 kB] Get:108 http://mirror.einval.org/debian sid/main i386 libblas-dev i386 3.9.0-3 [157 kB] Get:109 http://mirror.einval.org/debian sid/main i386 liblapack-dev i386 3.9.0-3 [3759 kB] Get:110 http://mirror.einval.org/debian sid/main i386 libarpack2-dev i386 3.8.0-1 [123 kB] Get:111 http://mirror.einval.org/debian sid/main i386 zlib1g i386 1:1.2.11.dfsg-2 [93.1 kB] Get:112 http://mirror.einval.org/debian sid/main i386 libhdf5-103-1 i386 1.10.6+repack-4 [1156 kB] Get:113 http://mirror.einval.org/debian sid/main i386 libhdf5-fortran-102 i386 1.10.6+repack-4 [114 kB] Get:114 http://mirror.einval.org/debian sid/main i386 libhdf5-hl-100 i386 1.10.6+repack-4 [93.2 kB] Get:115 http://mirror.einval.org/debian sid/main i386 libhdf5-hl-fortran-100 i386 1.10.6+repack-4 [58.3 kB] Get:116 http://mirror.einval.org/debian sid/main i386 libhdf5-cpp-103-1 i386 1.10.6+repack-4 [148 kB] Get:117 http://mirror.einval.org/debian sid/main i386 libhdf5-hl-cpp-100 i386 1.10.6+repack-4 [38.1 kB] Get:118 http://mirror.einval.org/debian sid/main i386 linux-libc-dev i386 5.10.46-1 [1361 kB] Get:119 http://mirror.einval.org/debian sid/main i386 libcrypt-dev i386 1:4.4.18-4 [116 kB] Get:120 http://mirror.einval.org/debian sid/main i386 libcom-err2 i386 1.46.2-2 [74.6 kB] Get:121 http://mirror.einval.org/debian sid/main i386 libkrb5support0 i386 1.18.3-5 [68.4 kB] Get:122 http://mirror.einval.org/debian sid/main i386 libk5crypto3 i386 1.18.3-5 [117 kB] Get:123 http://mirror.einval.org/debian sid/main i386 libkeyutils1 i386 1.6.1-2 [15.9 kB] Get:124 http://mirror.einval.org/debian sid/main i386 libssl1.1 i386 1.1.1k-1 [1550 kB] Get:125 http://mirror.einval.org/debian sid/main i386 libkrb5-3 i386 1.18.3-5 [390 kB] Get:126 http://mirror.einval.org/debian sid/main i386 libgssapi-krb5-2 i386 1.18.3-5 [176 kB] Get:127 http://mirror.einval.org/debian sid/main i386 libtirpc3 i386 1.3.1-1 [90.8 kB] Get:128 http://mirror.einval.org/debian sid/main i386 libnsl2 i386 1.3.0-2 [42.2 kB] Get:129 http://mirror.einval.org/debian sid/main i386 libtirpc-dev i386 1.3.1-1 [201 kB] Get:130 http://mirror.einval.org/debian sid/main i386 libnsl-dev i386 1.3.0-2 [70.6 kB] Get:131 http://mirror.einval.org/debian sid/main i386 libc6-dev i386 2.31-12 [3776 kB] Get:132 http://mirror.einval.org/debian sid/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get:133 http://mirror.einval.org/debian sid/main i386 libjpeg62-turbo i386 1:2.0.6-4 [160 kB] Get:134 http://mirror.einval.org/debian sid/main i386 libjpeg62-turbo-dev i386 1:2.0.6-4 [299 kB] Get:135 http://mirror.einval.org/debian sid/main i386 libjpeg-dev i386 1:2.0.6-4 [67.8 kB] Get:136 http://mirror.einval.org/debian sid/main i386 libhdf5-dev i386 1.10.6+repack-4 [2586 kB] Get:137 http://mirror.einval.org/debian sid/main i386 libsuperlu-dev i386 5.2.2+dfsg1-2 [21.4 kB] Get:138 http://mirror.einval.org/debian sid/main i386 libarmadillo-dev i386 1:10.1.2+dfsg-6 [386 kB] Get:139 http://mirror.einval.org/debian sid/main i386 libasan6 i386 10.2.1-6 [1930 kB] Get:140 http://mirror.einval.org/debian sid/main i386 libatomic1 i386 10.2.1-6 [9508 B] Get:141 http://mirror.einval.org/debian sid/main i386 libbamtools2.5.1 i386 2.5.1+dfsg-9 [176 kB] Get:142 http://mirror.einval.org/debian sid/main i386 libbamtools-dev i386 2.5.1+dfsg-9 [230 kB] Get:143 http://mirror.einval.org/debian sid/main i386 libgomp1 i386 10.2.1-6 [106 kB] Get:144 http://mirror.einval.org/debian sid/main i386 libitm1 i386 10.2.1-6 [28.6 kB] Get:145 http://mirror.einval.org/debian sid/main i386 libubsan1 i386 10.2.1-6 [752 kB] Get:146 http://mirror.einval.org/debian sid/main i386 libgcc-10-dev i386 10.2.1-6 [2324 kB] Get:147 http://mirror.einval.org/debian sid/main i386 libstdc++-10-dev i386 10.2.1-6 [1786 kB] Get:148 http://mirror.einval.org/debian sid/main i386 libboost1.74-dev i386 1.74.0-9 [9534 kB] Get:149 http://mirror.einval.org/debian sid/main i386 libboost-math1.74.0 i386 1.74.0-9 [464 kB] Get:150 http://mirror.einval.org/debian sid/main i386 libboost-math1.74-dev i386 1.74.0-9 [568 kB] Get:151 http://mirror.einval.org/debian sid/main i386 libboost-math-dev i386 1.74.0.3 [4536 B] Get:152 http://mirror.einval.org/debian sid/main i386 libdisorder0 i386 0.0.2+git20130809.8062ee1-2 [4392 B] Get:153 http://mirror.einval.org/debian sid/main i386 libdisorder-dev i386 0.0.2+git20130809.8062ee1-2 [4396 B] Get:154 http://mirror.einval.org/debian sid/main i386 libjsoncpp24 i386 1.9.4-4 [86.1 kB] Get:155 http://mirror.einval.org/debian sid/main i386 libjsoncpp-dev i386 1.9.4-4 [25.4 kB] Get:156 http://mirror.einval.org/debian sid/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-11 [38.6 kB] Get:157 http://mirror.einval.org/debian sid/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-11 [42.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 232 MB in 3s (66.7 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12271 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../001-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../003-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../005-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... 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Selecting previously unselected package libmagic-mgc. Preparing to unpack .../012-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../013-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../014-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../015-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../017-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. 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Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../036-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package libjsoncpp24:arm64. Preparing to unpack .../037-libjsoncpp24_1.9.4-4_arm64.deb ... Unpacking libjsoncpp24:arm64 (1.9.4-4) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../038-librhash0_1.4.1-2_arm64.deb ... Unpacking librhash0:arm64 (1.4.1-2) ... Selecting previously unselected package libuv1:arm64. Preparing to unpack .../039-libuv1_1.40.0-1_arm64.deb ... Unpacking libuv1:arm64 (1.40.0-1) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.18.4-2_arm64.deb ... Unpacking cmake (3.18.4-2) ... Selecting previously unselected package gcc-10-i686-linux-gnu-base:arm64. Preparing to unpack .../041-gcc-10-i686-linux-gnu-base_10.2.1-6cross1_arm64.deb ... Unpacking gcc-10-i686-linux-gnu-base:arm64 (10.2.1-6cross1) ... Selecting previously unselected package cpp-10-i686-linux-gnu. Preparing to unpack .../042-cpp-10-i686-linux-gnu_10.2.1-6cross1_arm64.deb ... Unpacking cpp-10-i686-linux-gnu (10.2.1-6cross1) ... Selecting previously unselected package cpp-i686-linux-gnu. Preparing to unpack .../043-cpp-i686-linux-gnu_4%3a10.2.1-1_arm64.deb ... Unpacking cpp-i686-linux-gnu (4:10.2.1-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../044-cross-config_2.6.18+nmu1_all.deb ... Unpacking cross-config (2.6.18+nmu1) ... Selecting previously unselected package binutils-i686-linux-gnu. Preparing to unpack .../045-binutils-i686-linux-gnu_2.35.2-2_arm64.deb ... Unpacking binutils-i686-linux-gnu (2.35.2-2) ... Selecting previously unselected package gcc-10-cross-base. Preparing to unpack .../046-gcc-10-cross-base_10.2.1-6cross1_all.deb ... Unpacking gcc-10-cross-base (10.2.1-6cross1) ... Selecting previously unselected package libc6-i386-cross. Preparing to unpack .../047-libc6-i386-cross_2.31-9cross4_all.deb ... Unpacking libc6-i386-cross (2.31-9cross4) ... Selecting previously unselected package libgcc-s1-i386-cross. Preparing to unpack .../048-libgcc-s1-i386-cross_10.2.1-6cross1_all.deb ... Unpacking libgcc-s1-i386-cross (10.2.1-6cross1) ... Selecting previously unselected package libgomp1-i386-cross. Preparing to unpack .../049-libgomp1-i386-cross_10.2.1-6cross1_all.deb ... Unpacking libgomp1-i386-cross (10.2.1-6cross1) ... Selecting previously unselected package libitm1-i386-cross. Preparing to unpack .../050-libitm1-i386-cross_10.2.1-6cross1_all.deb ... Unpacking libitm1-i386-cross (10.2.1-6cross1) ... Selecting previously unselected package libatomic1-i386-cross. Preparing to unpack .../051-libatomic1-i386-cross_10.2.1-6cross1_all.deb ... Unpacking libatomic1-i386-cross (10.2.1-6cross1) ... Selecting previously unselected package libasan6-i386-cross. 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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:i386 (1.10.6+repack-4) ... Setting up libicu67:arm64 (67.1-6) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up binutils-i686-linux-gnu (2.35.2-2) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up linux-libc-dev:i386 (5.10.46-1) ... Setting up libxml-namespacesupport-perl (1.12-1.1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libyaml-perl (1.30-1) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up libxml-sax-base-perl (1.09-1.1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up gcc-10-base:i386 (10.2.1-6) ... Setting up linux-libc-dev-i386-cross (5.10.13-1cross4) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up cross-config (2.6.18+nmu1) ... Setting up libuv1:arm64 (1.40.0-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libncursesw6:arm64 (6.2+20201114-2) ... Setting up gcc-10-cross-base (10.2.1-6cross1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up libjsoncpp24:arm64 (1.9.4-4) ... Setting up sensible-utils (0.0.14) ... Setting up librhash0:arm64 (1.4.1-2) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libc6-i386-cross (2.31-9cross4) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-3) ... Setting up cmake-data (3.18.4-2) ... Setting up gcc-10-i686-linux-gnu-base:arm64 (10.2.1-6cross1) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up libquadmath0-i386-cross (10.2.1-6cross1) ... Setting up libelf1:arm64 (0.183-3) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libprocps8:arm64 (2:3.3.17-5) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libatomic1-i386-cross (10.2.1-6cross1) ... Setting up libarchive13:arm64 (3.4.3-2+b1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libgomp1-i386-cross (10.2.1-6cross1) ... Setting up libc6-dev-i386-cross (2.31-9cross4) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgcc-s1-i386-cross (10.2.1-6cross1) ... Setting up libasan6-i386-cross (10.2.1-6cross1) ... Setting up cpp-10-i686-linux-gnu (10.2.1-6cross1) ... Setting up libitm1-i386-cross (10.2.1-6cross1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:arm64 (7.74.0-1.3) ... Setting up cpp-i686-linux-gnu (4:10.2.1-1) ... 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 po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++6-i386-cross (10.2.1-6cross1) ... Setting up dh-autoreconf (20) ... 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 cmake (3.18.4-2) ... Setting up debhelper (13.3.4) ... Setting up libubsan1-i386-cross (10.2.1-6cross1) ... Setting up libgcc-10-dev-i386-cross (10.2.1-6cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libstdc++-10-dev-i386-cross (10.2.1-6cross1) ... Setting up gcc-10-i686-linux-gnu (10.2.1-6cross1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up gcc-i686-linux-gnu (4:10.2.1-1) ... Setting up g++-10-i686-linux-gnu (10.2.1-6cross1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu1) ... Setting up g++-i686-linux-gnu (4:10.2.1-1) ... Setting up dpkg-cross (2.6.18+nmu1) ... Setting up crossbuild-essential-i386 (12.9) ... Setting up libgcc-s1:i386 (10.2.1-6) ... Setting up libcrypt1:i386 (1:4.4.18-4) ... Setting up libc6:i386 (2.31-12) ... Setting up libcrypt-dev:i386 (1:4.4.18-4) ... Setting up libstdc++6:i386 (10.2.1-6) ... Setting up libitm1:i386 (10.2.1-6) ... Setting up libdisorder0:i386 (0.0.2+git20130809.8062ee1-2) ... Setting up libkeyutils1:i386 (1.6.1-2) ... Setting up libssl1.1:i386 (1.1.1k-1) ... Setting up libsmithwaterman0:i386 (0.0+git20160702.2610e25-11) ... Setting up zlib1g:i386 (1:1.2.11.dfsg-2) ... Setting up libcom-err2:i386 (1.46.2-2) ... Setting up libgomp1:i386 (10.2.1-6) ... Setting up libaec0:i386 (1.0.4-3) ... Setting up libasan6:i386 (10.2.1-6) ... Setting up libkrb5support0:i386 (1.18.3-5) ... Setting up libblas3:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libjpeg62-turbo:i386 (1:2.0.6-4) ... Setting up libquadmath0:i386 (10.2.1-6) ... Setting up libbamtools2.5.1:i386 (2.5.1+dfsg-9) ... Setting up libatomic1:i386 (10.2.1-6) ... Setting up libk5crypto3:i386 (1.18.3-5) ... Setting up libdisorder-dev:i386 (0.0.2+git20130809.8062ee1-2) ... Setting up libgfortran5:i386 (10.2.1-6) ... Setting up libjsoncpp24:i386 (1.9.4-4) ... Setting up libboost-math1.74.0:i386 (1.74.0-9) ... Setting up libubsan1:i386 (10.2.1-6) ... Setting up libkrb5-3:i386 (1.18.3-5) ... Setting up libblas-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libsz2:i386 (1.0.4-3) ... Setting up libjsoncpp-dev:i386 (1.9.4-4) ... Setting up liblapack3:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libgcc-10-dev:i386 (10.2.1-6) ... Setting up libaec-dev:i386 (1.0.4-3) ... Setting up libarpack2:i386 (3.8.0-1) ... Setting up libsuperlu5:i386 (5.2.2+dfsg1-2) ... Setting up libbamtools-dev:i386 (2.5.1+dfsg-9) ... Setting up liblapack-dev:i386 (3.9.0-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up libgssapi-krb5-2:i386 (1.18.3-5) ... Setting up libsmithwaterman-dev:i386 (0.0+git20160702.2610e25-11) ... Setting up libhdf5-103-1:i386 (1.10.6+repack-4) ... Setting up libhdf5-cpp-103-1:i386 (1.10.6+repack-4) ... Setting up libsuperlu-dev:i386 (5.2.2+dfsg1-2) ... Setting up libhdf5-hl-100:i386 (1.10.6+repack-4) ... Setting up libtirpc3:i386 (1.3.1-1) ... Setting up libarmadillo10:i386 (1:10.1.2+dfsg-6) ... Setting up libarpack2-dev:i386 (3.8.0-1) ... Setting up libhdf5-hl-cpp-100:i386 (1.10.6+repack-4) ... Setting up libtirpc-dev:i386 (1.3.1-1) ... Setting up libhdf5-fortran-102:i386 (1.10.6+repack-4) ... Setting up libnsl2:i386 (1.3.0-2) ... Setting up libhdf5-hl-fortran-100:i386 (1.10.6+repack-4) ... Setting up libnsl-dev:i386 (1.3.0-2) ... Setting up libc6-dev:i386 (2.31-12) ... Setting up libstdc++-10-dev:i386 (10.2.1-6) ... Setting up libboost1.74-dev:i386 (1.74.0-9) ... Setting up libjpeg62-turbo-dev:i386 (1:2.0.6-4) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2) ... Setting up libboost-math1.74-dev:i386 (1.74.0-9) ... Setting up libboost-math-dev:i386 (1.74.0.3) ... Setting up libjpeg-dev:i386 (1:2.0.6-4) ... Setting up libhdf5-dev:i386 (1.10.6+repack-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/i386-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libarmadillo-dev:i386 (1:10.1.2+dfsg-6) ... Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.31-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (i386 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64) Toolchain package versions: binutils_2.35.2-2 dpkg-dev_1.20.9 g++-10_10.2.1-6 gcc-10_10.2.1-6 libc6-dev_2.31-12 libstdc++-10-dev_10.2.1-6 libstdc++-10-dev-i386-cross_10.2.1-6cross1 libstdc++6_10.2.1-6 libstdc++6-i386-cross_10.2.1-6cross1 linux-libc-dev_5.10.46-1 Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1 base-passwd_3.5.50 bash_5.1-3 binutils_2.35.2-2 binutils-aarch64-linux-gnu_2.35.2-2 binutils-common_2.35.2-2 binutils-i686-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 cpp_4:10.2.1-1 cpp-10_10.2.1-6 cpp-10-i686-linux-gnu_10.2.1-6cross1 cpp-i686-linux-gnu_4:10.2.1-1 cross-config_2.6.18+nmu1 crossbuild-essential-i386_12.9 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.3.4 debian-archive-keyring_2021.1.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dpkg_1.20.9 dpkg-cross_2.6.18+nmu1 dpkg-dev_1.20.9 dwz_0.14-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1 g++-10_10.2.1-6 g++-10-i686-linux-gnu_10.2.1-6cross1 g++-i686-linux-gnu_4:10.2.1-1 gcc_4:10.2.1-1 gcc-10_10.2.1-6 gcc-10-base_10.2.1-6 gcc-10-cross-base_10.2.1-6cross1 gcc-10-i686-linux-gnu_10.2.1-6cross1 gcc-10-i686-linux-gnu-base_10.2.1-6cross1 gcc-i686-linux-gnu_4:10.2.1-1 gettext_0.21-4 gettext-base_0.21-4 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hdf5-helpers_1.10.6+repack-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libaec-dev_1.0.4-3 libaec0_1.0.4-3 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2+b1 libarmadillo-dev_1:10.1.2+dfsg-6 libarmadillo10_1:10.1.2+dfsg-6 libarpack2_3.8.0-1 libarpack2-dev_3.8.0-1 libasan6_10.2.1-6 libasan6-i386-cross_10.2.1-6cross1 libatomic1_10.2.1-6 libatomic1-i386-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-9 libbamtools2.5.1_2.5.1+dfsg-9 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_2.31-12 libc-dev-bin_2.31-12 libc6_2.31-12 libc6-dev_2.31-12 libc6-dev-i386-cross_2.31-9cross4 libc6-i386-cross_2.31-9cross4 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6 libcom-err2_1.46.2-2 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2 libctf0_2.35.2-2 libcurl4_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.259 libdebhelper-perl_13.3.4 libdebian-dpkgcross-perl_2.6.18+nmu1 libdisorder-dev_0.0.2+git20130809.8062ee1-2 libdisorder0_0.0.2+git20130809.8062ee1-2 libdpkg-perl_1.20.9 libelf1_0.183-3 libexpat1_2.2.10-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.12.0-1 libfile-which-perl_1.23-1 libgcc-10-dev_10.2.1-6 libgcc-10-dev-i386-cross_10.2.1-6cross1 libgcc-s1_10.2.1-6 libgcc-s1-i386-cross_10.2.1-6cross1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_10.2.1-6 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6 libgomp1-i386-cross_10.2.1-6cross1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-5 libhdf5-103-1_1.10.6+repack-4 libhdf5-cpp-103-1_1.10.6+repack-4 libhdf5-dev_1.10.6+repack-4 libhdf5-fortran-102_1.10.6+repack-4 libhdf5-hl-100_1.10.6+repack-4 libhdf5-hl-cpp-100_1.10.6+repack-4 libhdf5-hl-fortran-100_1.10.6+repack-4 libhogweed6_3.7.3-1 libicu67_67.1-6 libidn2-0_2.3.0-5 libio-string-perl_1.08-3.1 libisl23_0.23-1 libitm1_10.2.1-6 libitm1-i386-cross_10.2.1-6cross1 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_1.18.3-5 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-5 libkrb5support0_1.18.3-5 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 liblsan0_10.2.1-6 liblz4-1_1.9.3-2 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_3.7.3-1 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_5.32.1-4 libpipeline1_1.5.3-1 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libquadmath0_10.2.1-6 libquadmath0-i386-cross_10.2.1-6cross1 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 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 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++-10-dev-i386-cross_10.2.1-6cross1 libstdc++6_10.2.1-6 libstdc++6-i386-cross_10.2.1-6cross1 libsub-override-perl_0.09-2 libsuperlu-dev_5.2.2+dfsg1-2 libsuperlu5_5.2.2+dfsg1-2 libsystemd0_247.3-5 libsz2_1.0.4-3 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 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xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: tvc Binary: tvc Architecture: any Version: 5.0.3+git20151221.80e144e+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Dominique Belhachemi , Andreas Tille Homepage: http://ioncommunity.thermofisher.com Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev Package-List: tvc deb science optional arch=any Checksums-Sha1: cd0223b1b1c96a2cc5a25fbc64e4e36a00347788 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 784aa00453ced25b09efc46ed91b140cf1dc7868 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz Checksums-Sha256: 3339f118d2fe983bc028630d5bf5238b6e91b70a85e8046a742588a6c342740c 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 8fa0c2fdd8670beb4b0ab726141010e619e4763d70ef292ab137c9bd12b9b506 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz Files: 68b468ca5054fb3260ad9de40131b632 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz be57abece3e5487df0f6939a38242aa7 8968 tvc_5.0.3+git20151221.80e144e+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCAAwFiEEkOLSwa0Uaht+u4kdu8F+uxOW8vcFAl5bTWkSHHN0dWFydEBk ZWJpYW4ub3JnAAoJELvBfrsTlvL3Wj0P/RPA3/JDLENaPvS8Z+hQOy/cIri64NFA ezi2Zl49RMqHyajLaT1CW3o/iDdXd4aweLbbvmfLrCjucRMdplm6RBQTPn9Ev1dj 1ja4LQJyxENqJqHWGdOL6dt9RCHIahMZYTV7LSaTaDk9f3QW0RREPbXrm/pD3uJu +PosQld9epddEd/T9zBcZIVPmUeW2oDue5k8TPspJcEeHVe1jRwM4eAuEeIvKYgg GItm/idx9b1jL+FcoIzCHeLo78nnIsKiHgbfw8+iexTFQ0ejh9A+cEp+LWpzISEj 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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 +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ ulimit -c --------- 0 I: Finished running 'ulimit -c'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.i386 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmutg PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=crossqa-sid SCHROOT_CHROOT_NAME=crossqa-sid SCHROOT_COMMAND=env SCHROOT_GID=1002 SCHROOT_GROUP=helmutg SCHROOT_SESSION_ID=crossqa-sid-cbb58e6a-e1b0-4f47-9901-14d2e2dcc4bd SCHROOT_UID=1002 SCHROOT_USER=helmutg SHELL=/bin/sh USER=helmutg dpkg-buildpackage ----------------- Command: dpkg-buildpackage -ai386 -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 i686-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 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-i686-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=i686 -DCMAKE_C_COMPILER=i686-linux-gnu-gcc -DCMAKE_CXX_COMPILER=i686-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/i686-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/i686-linux-gnu-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/i686-linux-gnu-qmake -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/i686-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/i686-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE QMAKE_EXECUTABLE -- Build files have been written to: /<>/obj-i686-linux-gnu dh_auto_build -a cd obj-i686-linux-gnu && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-i686-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-i686-linux-gnu/CMakeFiles /<>/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-i686-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/<>/obj-i686-linux-gnu' cd /<>/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= Dependee "/<>/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake" is newer than depender "/<>/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/depend.internal". 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Scanning dependencies of target tvcassembly make[3]: Leaving directory '/<>/obj-i686-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/obj-i686-linux-gnu' [ 21%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o /usr/bin/i686-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/i686-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/i686-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/i686-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/i686-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/i686-linux-gnu/include/string.h:495, from /usr/i686-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/i686-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/Util/Utils.cpp: In function ‘char* GetProcessParam(const char*, const char*)’: /<>/Util/Utils.cpp:503:37: note: length computed here 503 | strncpy (keyword, buf, strlen (buf)-1); | ~~~~~~~^~~~~ [ 29%] Building CXX object CMakeFiles/tvcassembly.dir/IonVersion.cpp.o /usr/bin/i686-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-i686-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/i686-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-i686-linux-gnu' [ 31%] Built target tvcassembly make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/<>/obj-i686-linux-gnu' cd /<>/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= Dependee "/<>/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake" is newer than depender "/<>/obj-i686-linux-gnu/CMakeFiles/tvc.dir/depend.internal". 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Scanning dependencies of target tvc make[3]: Leaving directory '/<>/obj-i686-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/obj-i686-linux-gnu' [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o /usr/bin/i686-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/i686-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/i686-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 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CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/i686-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/TargetsManager.cpp.o -c /<>/VariantCaller/TargetsManager.cpp [ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o /usr/bin/i686-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/HandleVariant.cpp.o -c /<>/VariantCaller/HandleVariant.cpp [ 42%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o /usr/bin/i686-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/HotspotReader.cpp.o -c /<>/VariantCaller/HotspotReader.cpp [ 43%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/i686-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/MetricsManager.cpp.o -c /<>/VariantCaller/MetricsManager.cpp [ 45%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o /usr/bin/i686-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/Bookkeeping/MiscUtil.cpp.o -c /<>/VariantCaller/Bookkeeping/MiscUtil.cpp [ 46%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o /usr/bin/i686-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/Bookkeeping/ExtendParameters.cpp.o -c /<>/VariantCaller/Bookkeeping/ExtendParameters.cpp [ 48%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o /usr/bin/i686-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/Bookkeeping/InputStructures.cpp.o -c /<>/VariantCaller/Bookkeeping/InputStructures.cpp /<>/VariantCaller/Bookkeeping/InputStructures.cpp: In member function ‘void RecalibrationHandler::ReadRecalibrationFromComments(const BamTools::SamHeader&, const std::map, int>&)’: /<>/VariantCaller/Bookkeeping/InputStructures.cpp:240:18: warning: ‘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: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/i686-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/Bookkeeping/VcfFormat.cpp.o -c /<>/VariantCaller/Bookkeeping/VcfFormat.cpp [ 51%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o /usr/bin/i686-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/Reads/ExtendedReadInfo.cpp.o -c /<>/VariantCaller/Reads/ExtendedReadInfo.cpp [ 53%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o /usr/bin/i686-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/Splice/ErrorMotifs.cpp.o -c /<>/VariantCaller/Splice/ErrorMotifs.cpp [ 54%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o /usr/bin/i686-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/Splice/LocalContext.cpp.o -c /<>/VariantCaller/Splice/LocalContext.cpp [ 56%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o /usr/bin/i686-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/Splice/ClassifyVariant.cpp.o -c /<>/VariantCaller/Splice/ClassifyVariant.cpp [ 57%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o /usr/bin/i686-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/Splice/SpliceVariantHypotheses.cpp.o -c /<>/VariantCaller/Splice/SpliceVariantHypotheses.cpp [ 59%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o /usr/bin/i686-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/Filter/DecisionTreeData.cpp.o -c /<>/VariantCaller/Filter/DecisionTreeData.cpp [ 60%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o /usr/bin/i686-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/Filter/VariantAssist.cpp.o -c /<>/VariantCaller/Filter/VariantAssist.cpp /<>/VariantCaller/Filter/VariantAssist.cpp: In function ‘double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)’: /<>/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] 191 | fprintf(stdout, "ref.size()=%lu; ", ref.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /<>/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] 192 | fprintf(stdout, "var.size()=%lu; ", var.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /<>/VariantCaller/Filter/VariantAssist.cpp:193:37: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] 193 | fprintf(stdout, "both.size()=%lu; ", both.size()); | ~~^ ~~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u [ 62%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o /usr/bin/i686-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/HypothesisEvaluator.cpp.o -c /<>/VariantCaller/HypothesisEvaluator.cpp [ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o /usr/bin/i686-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/EnsembleEval/DiagnosticJSON.cpp.o -c /<>/VariantCaller/EnsembleEval/DiagnosticJSON.cpp [ 65%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o /usr/bin/i686-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=/<>=. 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-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/EnsembleEval/PosteriorInference.cpp.o -c /<>/VariantCaller/EnsembleEval/PosteriorInference.cpp [ 71%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o /usr/bin/i686-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 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-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/i686-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/i686-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/i686-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/i686-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/i686-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/i686-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/i686-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/i686-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/i686-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/Util/OptArgs.cpp.o -c /<>/Util/OptArgs.cpp [ 93%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o /usr/bin/i686-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/realignment/Realigner.cpp.o -c /<>/realignment/Realigner.cpp [ 95%] Building C object CMakeFiles/tvc.dir/file-io/ion_util.c.o /usr/bin/i686-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_util.c.o -c /<>/file-io/ion_util.c [ 96%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o /usr/bin/i686-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/i686-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-i686-linux-gnu/IonVersion.cpp [100%] Linking CXX executable tvc /usr/bin/cmake -E cmake_link_script CMakeFiles/tvc.dir/link.txt --verbose=1 /usr/bin/i686-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/tvc.dir/VariantCaller/VariantCaller.cpp.o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o 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-i686-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/<>/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-i686-linux-gnu' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a cd obj-i686-linux-gnu && make -j1 install DESTDIR=/<>/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-i686-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-i686-linux-gnu/CMakeFiles /<>/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-i686-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/<>/obj-i686-linux-gnu' cd /<>/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-i686-linux-gnu' make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/<>/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcutils.dir/build'. make[3]: Leaving directory '/<>/obj-i686-linux-gnu' [ 20%] Built target tvcutils make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/<>/obj-i686-linux-gnu' cd /<>/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-i686-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Entering directory '/<>/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvcassembly.dir/build'. make[3]: Leaving directory '/<>/obj-i686-linux-gnu' [ 31%] Built target tvcassembly make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/<>/obj-i686-linux-gnu' cd /<>/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu /<>/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-i686-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/tvc.dir/build'. make[3]: Leaving directory '/<>/obj-i686-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/<>/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-i686-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-i686-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/pgx4_germline_lowstringency_pgm_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/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_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/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_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/reference.fasta -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bed -- 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 -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/reference.dict make[1]: Leaving directory '/<>/obj-i686-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_i386.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_i386.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../tvc_5.0.3+git20151221.80e144e+dfsg-3_i386.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 2021-06-27T05:43:32Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ tvc_5.0.3+git20151221.80e144e+dfsg-3_i386.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: i386 Version: 5.0.3+git20151221.80e144e+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Stuart Prescott Description: tvc - genetic variant caller for Ion Torrent sequencing platforms Closes: 945720 Changes: tvc (5.0.3+git20151221.80e144e+dfsg-3) unstable; urgency=medium . * Team upload. * Use Python 3 in scripts (Closes: #945720). * Add Rules-Requires-Root: no. * Update Standards-Version to 4.5.0 (no changes required). * Switch to debhelper-compat (= 12). 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+------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-3_i386.deb ---------------------------------------------------- new Debian package, version 2.0. size 10416576 bytes: control archive=704 bytes. 487 bytes, 12 lines control 396 bytes, 4 lines md5sums Package: tvc-dbgsym Source: tvc Version: 5.0.3+git20151221.80e144e+dfsg-3 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 10512 Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-3) Section: debug Priority: optional Description: debug symbols for tvc Build-Ids: a73bec098e529eb8d4e1a8fb02af062c06b9f4f0 cd4d33f794152b9ee3051a0e2eb786d18a3e4d14 fe947fd011af03daae68eb3da93d3fa4641334d6 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/a7/ -rw-r--r-- root/root 7263672 2020-03-01 04:57 ./usr/lib/debug/.build-id/a7/3bec098e529eb8d4e1a8fb02af062c06b9f4f0.debug drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/cd/ -rw-r--r-- root/root 2277612 2020-03-01 04:57 ./usr/lib/debug/.build-id/cd/4d33f794152b9ee3051a0e2eb786d18a3e4d14.debug drwxr-xr-x root/root 0 2020-03-01 04:57 ./usr/lib/debug/.build-id/fe/ -rw-r--r-- root/root 759740 2020-03-01 04:57 ./usr/lib/debug/.build-id/fe/947fd011af03daae68eb3da93d3fa4641334d6.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/i386-linux-gnu/ -rw-r--r-- root/root 446496 2020-03-01 04:57 ./usr/lib/debug/.dwz/i386-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_i386.deb --------------------------------------------- new Debian package, version 2.0. size 1103640 bytes: control archive=1676 bytes. 992 bytes, 16 lines control 2459 bytes, 28 lines md5sums Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-3 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 3421 Depends: libarmadillo10 (>= 1:10.1.2+dfsg), libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.29), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 3.0), 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 1187860 2020-03-01 04:57 ./usr/bin/tvc -rwxr-xr-x root/root 219412 2020-03-01 04:57 ./usr/bin/tvcassembly -rwxr-xr-x root/root 645716 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:arm64 Filtered Build-Depends: lintian:arm64 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 [576 B] Get:5 copy:/<>/apt_archive ./ Packages [664 B] Fetched 2203 B in 0s (52.6 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:i386 t1utils unzip 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 7453 kB of archives. After this operation, 21.4 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://mirror.einval.org/debian sid/main arm64 readline-common all 8.1-2 [73.8 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1-2 [160 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 diffstat arm64 1.64-1 [34.6 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 libassuan0 arm64 2.5.4-1 [48.7 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 gpgconf arm64 2.2.27-2 [540 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.34.1-3 [750 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.27-2 [883 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libaliased-perl all 0.34-1.1 [14.1 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40 [69.4 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-1+b3 [11.2 kB] Get:12 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arm64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-2 [36.8 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-1+b1 [25.3 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.110-1.1 [10.8 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.987-1 [47.2 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.00-4+b1 [37.6 kB] Get:41 http://mirror.einval.org/debian sid/main 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[21.0 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.004004-1 [59.9 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b1 [170 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-1+b3 [11.9 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-1+b1 [13.5 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.118-1 [53.5 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.19-1+b7 [17.0 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.59-2+b1 [45.7 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 4.018+ds-1+b1 [95.3 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 4.018+ds-1+b1 [98.3 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-4+b8 [8680 B] Get:75 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.12-1+b1 [12.9 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.8-1+b1 [195 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-1+b3 [75.1 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libtype-tiny-perl all 1.012002-1 [351 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b2 [19.8 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.08-1 [90.6 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.82+repack-1+b1 [34.5 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 lzip arm64 1.22-3 [84.7 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-26 [165 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 lintian all 2.104.0 [1265 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7453 kB in 2s (4790 kB/s) Selecting previously unselected package readline-common. (Reading database ... 38236 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.1-2_all.deb ... Unpacking readline-common (8.1-2) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../01-libreadline8_8.1-2_arm64.deb ... Unpacking libreadline8:arm64 (8.1-2) ... Selecting previously unselected package diffstat. Preparing to unpack .../02-diffstat_1.64-1_arm64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../03-libassuan0_2.5.4-1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.4-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../04-gpgconf_2.2.27-2_arm64.deb ... Unpacking gpgconf (2.2.27-2) ... Selecting previously unselected package libsqlite3-0:arm64. Preparing to unpack .../05-libsqlite3-0_3.34.1-3_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.34.1-3) ... Selecting previously unselected package gpg. Preparing to unpack .../06-gpg_2.2.27-2_arm64.deb ... Unpacking gpg (2.2.27-2) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../07-libaliased-perl_0.34-1.1_all.deb ... Unpacking libaliased-perl (0.34-1.1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../08-libapt-pkg-perl_0.1.40_arm64.deb ... Unpacking libapt-pkg-perl (0.1.40) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../09-libb-hooks-op-check-perl_0.22-1+b3_arm64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b3) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../10-libdynaloader-functions-perl_0.003-1.1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1.1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../11-libdevel-callchecker-perl_0.008-1+b2_arm64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b2) ... 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Setting up libsqlite3-0:arm64 (3.34.1-3) ... Setting up libyaml-libyaml-perl (0.82+repack-1+b1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up liblzo2-2:arm64 (2.10-2) ... Setting up libtime-moment-perl (0.44-1+b3) ... Setting up libassuan0:arm64 (2.5.4-1) ... Setting up libconfig-tiny-perl (2.26-1) ... Setting up libsereal-encoder-perl (4.018+ds-1+b1) ... Setting up liblist-utilsby-perl (0.11-1) ... Setting up libsub-install-perl (0.928-1.1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004003-1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libnet-domain-tld-perl (1.75-1.1) ... Setting up lzip (1.22-3) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.62-1+b3) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up liblist-moreutils-xs-perl (0.430-2) ... Setting up libparams-util-perl (1.102-1+b1) ... Setting up libtime-duration-perl (1.21-1) ... Setting up libtext-xslate-perl (3.5.8-1+b1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl (0.26-1+b1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl (0.59-2+b1) ... Setting up libpath-tiny-perl (0.118-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-2) ... Setting up libaliased-perl (0.34-1.1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b7) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libfont-ttf-perl (1.06-1.1) ... Setting up libtext-levenshteinxs-perl (0.03-4+b8) ... Setting up libperlio-gzip-perl (0.19-1+b7) ... Setting up readline-common (8.1-2) ... Setting up libhtml-html5-entities-perl (0.004-1.1) ... Setting up libsereal-decoder-perl (4.018+ds-1+b1) ... Setting up libmarkdown2:arm64 (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:arm64 (8.1-2) ... Setting up libtype-tiny-perl (1.012002-1) ... Setting up libtext-markdown-discount-perl:arm64 (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 (2.2.27-2) ... Setting up gpg (2.2.27-2) ... 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:i386 (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 (2.31-12) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 148168 Build-Time: 733 Distribution: unstable Foreign Architectures: i386 Host Architecture: i386 Install-Time: 71 Job: tvc_5.0.3+git20151221.80e144e+dfsg-3 Lintian: pass Machine Architecture: arm64 Package: tvc Package-Time: 833 Source-Version: 5.0.3+git20151221.80e144e+dfsg-3 Space: 148168 Status: successful Version: 5.0.3+git20151221.80e144e+dfsg-3 -------------------------------------------------------------------------------- Finished at 2021-06-27T05:43:32Z Build needed 00:13:53, 148168k disk space