sbuild (Debian sbuild) 0.81.2+deb11u1 (31 August 2022) on debian-ci-siliconvalley +==============================================================================+ | tvc 5.0.3+git20151221.80e144e+dfsg-5 (armel) Sun, 04 Dec 2022 16:53:09 +0000 | +==============================================================================+ Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-5 Source Version: 5.0.3+git20151221.80e144e+dfsg-5 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-bb3bf4b6-72f7-4375-9080-e21747b56759' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-UxfNuX/resolver-Wr15ME' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [161 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2022-12-04-1405.06-F-2022-12-04-0205.35.pdiff [34.9 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2022-12-04-1405.06-F-2022-12-04-0205.35.pdiff [31.4 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2022-12-04-1405.06-F-2022-12-04-0205.35.pdiff [34.9 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2022-12-04-1405.06-F-2022-12-04-0205.35.pdiff [31.4 kB] Get:6 http://localhost:3142/debian sid/main armel Packages [8982 kB] Fetched 9337 kB in 3s (3525 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 757 kB of source archives. Get:1 http://localhost:3142/debian sid/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (dsc) [2227 B] Get:2 http://localhost:3142/debian sid/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (tar) [745 kB] Get:3 http://localhost:3142/debian sid/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (diff) [9800 B] Fetched 757 kB in 0s (14.8 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/tvc-UxfNuX/tvc-5.0.3+git20151221.80e144e+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/tvc-UxfNuX' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [445 B] Get:5 copy:/<>/apt_archive ./ Packages [536 B] Fetched 1938 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdextrautils cmake cmake-data cpp-12-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-12-arm-linux-gnueabi gcc-12-arm-linux-gnueabi-base gcc-12-base:armel gcc-12-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base hdf5-helpers:armel intltool-debian libaec-dev:armel libaec0:armel libarchive-zip-perl libarchive13 libarmadillo-dev:armel libarmadillo11:armel libarpack2:armel libarpack2-dev:armel libasan8:armel libasan8-armel-cross libatomic1:armel libatomic1-armel-cross libbamtools-dev:armel libbamtools2.5.2:armel libblas-dev:armel libblas3:armel libboost-math-dev:armel libboost-math1.74-dev:armel libboost-math1.74.0:armel libboost1.74-dev:armel libbrotli1 libbrotli1:armel libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armel libcrypt1:armel libcurl4 libcurl4:armel libcurl4-openssl-dev:armel libdb5.3:armel libdebhelper-perl libdebian-dpkgcross-perl libdisorder-dev:armel libdisorder0:armel libelf1 libexpat1 libffi8:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-12-dev:armel libgcc-12-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgfortran5:armel libgmp10:armel libgnutls30:armel libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libhdf5-103-1:armel libhdf5-cpp-103-1:armel libhdf5-dev:armel libhdf5-fortran-102:armel libhdf5-hl-100:armel libhdf5-hl-cpp-100:armel libhdf5-hl-fortran-100:armel libhogweed6:armel libicu72 libidn2-0:armel libio-string-perl libjpeg-dev:armel libjpeg62-turbo:armel libjpeg62-turbo-dev:armel libjsoncpp-dev:armel libjsoncpp25 libjsoncpp25:armel libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel liblapack-dev:armel liblapack3:armel libldap-2.5-0 libldap-2.5-0:armel liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libncursesw6 libnettle8:armel libnghttp2-14 libnghttp2-14:armel libnsl-dev:armel libnsl2:armel libp11-kit0:armel libpipeline1 libprocps8 libpsl5 libpsl5:armel librhash0 librtmp1 librtmp1:armel libsasl2-2 libsasl2-2:armel libsasl2-modules-db libsasl2-modules-db:armel libsmithwaterman-dev:armel libsmithwaterman0:armel libssh2-1 libssh2-1:armel libssl-dev:armel libssl3:armel libstdc++-12-dev:armel libstdc++-12-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libsuperlu-dev:armel libsuperlu5:armel libsz2:armel libtasn1-6:armel libtirpc-dev:armel libtirpc3:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libunistring2:armel libuv1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:armel linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db po-debconf procps sensible-utils ucf zlib1g:armel zlib1g-dev:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc cmake-format elpa-cmake-mode ninja-build gcc-12-locales cpp-12-doc cpp-doc dh-make binutils-multiarch gcc-12-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libitpp-dev:armel libbamtools-doc:armel liblapack-doc:armel libboost1.74-doc:armel libboost-atomic1.74-dev:armel libboost-chrono1.74-dev:armel libboost-container1.74-dev:armel libboost-context1.74-dev:armel libboost-contract1.74-dev:armel libboost-coroutine1.74-dev:armel libboost-date-time1.74-dev:armel libboost-exception1.74-dev:armel libboost-fiber1.74-dev:armel libboost-filesystem1.74-dev:armel libboost-graph1.74-dev:armel libboost-graph-parallel1.74-dev:armel libboost-iostreams1.74-dev:armel libboost-locale1.74-dev:armel libboost-log1.74-dev:armel libboost-mpi1.74-dev:armel libboost-mpi-python1.74-dev:armel libboost-numpy1.74-dev:armel libboost-program-options1.74-dev:armel libboost-python1.74-dev:armel libboost-random1.74-dev:armel libboost-regex1.74-dev:armel libboost-serialization1.74-dev:armel libboost-stacktrace1.74-dev:armel libboost-system1.74-dev:armel libboost-test1.74-dev:armel libboost-thread1.74-dev:armel libboost-timer1.74-dev:armel libboost-type-erasure1.74-dev:armel libboost-wave1.74-dev:armel libboost1.74-tools-dev:armel libmpfrc++-dev:armel libntl-dev:armel libboost-nowide1.74-dev:armel glibc-doc:armel libc-l10n:armel locales:armel libnss-nis:armel libnss-nisplus:armel manpages-dev:armel libcurl4-doc:armel libidn11-dev:armel libkrb5-dev:armel libldap2-dev:armel librtmp-dev:armel libssh2-1-dev:armel pkg-config:armel gnutls-bin:armel krb5-doc:armel krb5-user:armel libhdf5-doc:armel libssl-doc:armel libstdc++-12-doc:armel libsuperlu-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx ca-certificates ca-certificates:armel libarchive-cpio-perl krb5-locales:armel libldap-common libldap-common:armel libgpm2 publicsuffix publicsuffix:armel libsasl2-modules libsasl2-modules:armel libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdextrautils cmake cmake-data cpp-12-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-12-arm-linux-gnueabi gcc-12-arm-linux-gnueabi-base gcc-12-base:armel gcc-12-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base hdf5-helpers:armel intltool-debian libaec-dev:armel libaec0:armel libarchive-zip-perl libarchive13 libarmadillo-dev:armel libarmadillo11:armel libarpack2:armel libarpack2-dev:armel libasan8:armel libasan8-armel-cross libatomic1:armel libatomic1-armel-cross libbamtools-dev:armel libbamtools2.5.2:armel libblas-dev:armel libblas3:armel libboost-math-dev:armel libboost-math1.74-dev:armel libboost-math1.74.0:armel libboost1.74-dev:armel libbrotli1 libbrotli1:armel libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armel libcrypt1:armel libcurl4 libcurl4:armel libcurl4-openssl-dev:armel libdb5.3:armel libdebhelper-perl libdebian-dpkgcross-perl libdisorder-dev:armel libdisorder0:armel libelf1 libexpat1 libffi8:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-12-dev:armel libgcc-12-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgfortran5:armel libgmp10:armel libgnutls30:armel libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libhdf5-103-1:armel libhdf5-cpp-103-1:armel libhdf5-dev:armel libhdf5-fortran-102:armel libhdf5-hl-100:armel libhdf5-hl-cpp-100:armel libhdf5-hl-fortran-100:armel libhogweed6:armel libicu72 libidn2-0:armel libio-string-perl libjpeg-dev:armel libjpeg62-turbo:armel libjpeg62-turbo-dev:armel libjsoncpp-dev:armel libjsoncpp25 libjsoncpp25:armel libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel liblapack-dev:armel liblapack3:armel libldap-2.5-0 libldap-2.5-0:armel liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libncursesw6 libnettle8:armel libnghttp2-14 libnghttp2-14:armel libnsl-dev:armel libnsl2:armel libp11-kit0:armel libpipeline1 libprocps8 libpsl5 libpsl5:armel librhash0 librtmp1 librtmp1:armel libsasl2-2 libsasl2-2:armel libsasl2-modules-db libsasl2-modules-db:armel libsmithwaterman-dev:armel libsmithwaterman0:armel libssh2-1 libssh2-1:armel libssl-dev:armel libssl3:armel libstdc++-12-dev:armel libstdc++-12-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libsuperlu-dev:armel libsuperlu5:armel libsz2:armel libtasn1-6:armel libtirpc-dev:armel libtirpc3:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libunistring2:armel libuv1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:armel linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db po-debconf procps sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel 0 upgraded, 174 newly installed, 0 to remove and 0 not upgraded. Need to get 129 MB of archives. After this operation, 620 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://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4+b3 [15.1 kB] Get:3 http://localhost:3142/debian sid/main amd64 libncurses6 amd64 6.3+20220423-2 [102 kB] Get:4 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.3+20220423-2 [133 kB] Get:5 http://localhost:3142/debian sid/main amd64 libprocps8 amd64 2:3.3.17-7.1 [45.1 kB] Get:6 http://localhost:3142/debian sid/main amd64 procps amd64 2:3.3.17-7.1 [482 kB] Get:7 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:8 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.41-4 [295 kB] Get:9 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.41-4 [129 kB] Get:10 http://localhost:3142/debian sid/main amd64 file amd64 1:5.41-4 [67.0 kB] Get:11 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-10 [160 kB] Get:12 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:13 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-9 [916 kB] Get:14 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38.1-4 [86.2 kB] Get:15 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:16 http://localhost:3142/debian sid/main amd64 man-db amd64 2.11.1-1 [1384 kB] Get:17 http://localhost:3142/debian sid/main amd64 ucf all 3.0043 [74.0 kB] Get:18 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-1 [291 kB] Get:19 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:20 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:21 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:22 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-10 [495 kB] Get:23 http://localhost:3142/debian sid/main amd64 binutils-arm-linux-gnueabi amd64 2.39-8 [3232 kB] Get:24 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:25 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b2 [687 kB] Get:26 http://localhost:3142/debian sid/main amd64 libarchive13 amd64 3.6.0-1 [350 kB] Get:27 http://localhost:3142/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b5 [279 kB] Get:28 http://localhost:3142/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:29 http://localhost:3142/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:30 http://localhost:3142/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-2+b1 [183 kB] Get:31 http://localhost:3142/debian sid/main amd64 libnghttp2-14 amd64 1.50.0-1+b1 [73.1 kB] Get:32 http://localhost:3142/debian sid/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:33 http://localhost:3142/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:34 http://localhost:3142/debian sid/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:35 http://localhost:3142/debian sid/main amd64 libcurl4 amd64 7.86.0-2 [364 kB] Get:36 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:37 http://localhost:3142/debian sid/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get:38 http://localhost:3142/debian sid/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get:39 http://localhost:3142/debian sid/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get:40 http://localhost:3142/debian sid/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get:41 http://localhost:3142/debian sid/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get:42 http://localhost:3142/debian sid/main amd64 gcc-12-arm-linux-gnueabi-base amd64 12.2.0-9cross2 [37.3 kB] Get:43 http://localhost:3142/debian sid/main amd64 cpp-12-arm-linux-gnueabi amd64 12.2.0-9cross2 [8663 kB] Get:44 http://localhost:3142/debian sid/main amd64 cpp-arm-linux-gnueabi amd64 4:12.2.0-1 [17.2 kB] Get:45 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.19 [16.3 kB] Get:46 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base all 12.2.0-9cross2 [32.8 kB] Get:47 http://localhost:3142/debian sid/main amd64 libc6-armel-cross all 2.36-3cross1 [885 kB] Get:48 http://localhost:3142/debian sid/main amd64 libgcc-s1-armel-cross all 12.2.0-9cross2 [38.4 kB] Get:49 http://localhost:3142/debian sid/main amd64 libgomp1-armel-cross all 12.2.0-9cross2 [96.8 kB] Get:50 http://localhost:3142/debian sid/main amd64 libatomic1-armel-cross all 12.2.0-9cross2 [8912 B] Get:51 http://localhost:3142/debian sid/main amd64 libasan8-armel-cross all 12.2.0-9cross2 [2092 kB] Get:52 http://localhost:3142/debian sid/main amd64 libstdc++6-armel-cross all 12.2.0-9cross2 [464 kB] Get:53 http://localhost:3142/debian sid/main amd64 libubsan1-armel-cross all 12.2.0-9cross2 [862 kB] Get:54 http://localhost:3142/debian sid/main amd64 libgcc-12-dev-armel-cross all 12.2.0-9cross2 [732 kB] Get:55 http://localhost:3142/debian sid/main amd64 gcc-12-arm-linux-gnueabi amd64 12.2.0-9cross2 [17.0 MB] Get:56 http://localhost:3142/debian sid/main amd64 gcc-arm-linux-gnueabi amd64 4:12.2.0-1 [1452 B] Get:57 http://localhost:3142/debian sid/main amd64 linux-libc-dev-armel-cross all 6.0.6-2cross1 [1763 kB] Get:58 http://localhost:3142/debian sid/main amd64 libc6-dev-armel-cross all 2.36-3cross1 [1284 kB] Get:59 http://localhost:3142/debian sid/main amd64 libstdc++-12-dev-armel-cross all 12.2.0-9cross2 [2033 kB] Get:60 http://localhost:3142/debian sid/main amd64 g++-12-arm-linux-gnueabi amd64 12.2.0-9cross2 [9594 kB] Get:61 http://localhost:3142/debian sid/main amd64 g++-arm-linux-gnueabi amd64 4:12.2.0-1 [1176 B] Get:62 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:63 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:64 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:65 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:66 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:67 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:68 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:69 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:70 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:71 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:72 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:73 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.19 [15.3 kB] Get:74 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.19 [25.6 kB] Get:75 http://localhost:3142/debian sid/main amd64 crossbuild-essential-armel all 12.9 [6704 B] Get:76 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.1 [80.8 kB] Get:77 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-5 [517 kB] Get:78 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:79 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:80 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get:81 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB] Get:82 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.0-2 [8556 B] Get:83 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.188-1 [172 kB] Get:84 http://localhost:3142/debian sid/main amd64 dwz amd64 0.14+20220924-2 [109 kB] Get:85 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-10 [1300 kB] Get:86 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:87 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:88 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.1 [941 kB] Get:89 http://localhost:3142/debian sid/main armel gcc-12-base armel 12.2.0-9 [37.1 kB] Get:90 http://localhost:3142/debian sid/main armel hdf5-helpers armel 1.10.8+repack-4 [27.8 kB] Get:91 http://localhost:3142/debian sid/main armel libgcc-s1 armel 12.2.0-9 [38.4 kB] Get:92 http://localhost:3142/debian sid/main armel libc6 armel 2.36-6 [2184 kB] Get:93 http://localhost:3142/debian sid/main armel libaec0 armel 1.0.6-1+b1 [19.6 kB] Get:94 http://localhost:3142/debian sid/main armel libsz2 armel 1.0.6-1+b1 [7872 B] Get:95 http://localhost:3142/debian sid/main armel libaec-dev armel 1.0.6-1+b1 [18.0 kB] Get:96 http://localhost:3142/debian sid/main armel libblas3 armel 3.11.0-2 [181 kB] Get:97 http://localhost:3142/debian sid/main armel libgfortran5 armel 12.2.0-9 [257 kB] Get:98 http://localhost:3142/debian sid/main armel liblapack3 armel 3.11.0-2 [2256 kB] Get:99 http://localhost:3142/debian sid/main armel libarpack2 armel 3.8.0-3 [97.5 kB] Get:100 http://localhost:3142/debian sid/main armel libstdc++6 armel 12.2.0-9 [506 kB] Get:101 http://localhost:3142/debian sid/main armel libsuperlu5 armel 5.3.0+dfsg1-2+b1 [167 kB] Get:102 http://localhost:3142/debian sid/main armel libarmadillo11 armel 1:11.4.2+dfsg-1 [96.3 kB] Get:103 http://localhost:3142/debian sid/main armel libblas-dev armel 3.11.0-2 [191 kB] Get:104 http://localhost:3142/debian sid/main armel liblapack-dev armel 3.11.0-2 [4457 kB] Get:105 http://localhost:3142/debian sid/main armel libarpack2-dev armel 3.8.0-3 [118 kB] Get:106 http://localhost:3142/debian sid/main armel libbrotli1 armel 1.0.9-2+b5 [283 kB] Get:107 http://localhost:3142/debian sid/main armel libcom-err2 armel 1.46.6~rc1-1+b1 [14.2 kB] Get:108 http://localhost:3142/debian sid/main armel libkrb5support0 armel 1.20.1-1 [29.2 kB] Get:109 http://localhost:3142/debian sid/main armel libk5crypto3 armel 1.20.1-1 [74.0 kB] Get:110 http://localhost:3142/debian sid/main armel libkeyutils1 armel 1.6.3-1 [14.8 kB] Get:111 http://localhost:3142/debian sid/main armel libatomic1 armel 12.2.0-9 [9152 B] Get:112 http://localhost:3142/debian sid/main armel libssl3 armel 3.0.7-1 [1621 kB] Get:113 http://localhost:3142/debian sid/main armel libkrb5-3 armel 1.20.1-1 [284 kB] Get:114 http://localhost:3142/debian sid/main armel libgssapi-krb5-2 armel 1.20.1-1 [110 kB] Get:115 http://localhost:3142/debian sid/main armel libunistring2 armel 1.0-2 [398 kB] Get:116 http://localhost:3142/debian sid/main armel libidn2-0 armel 2.3.3-1+b1 [120 kB] Get:117 http://localhost:3142/debian sid/main armel libgmp10 armel 2:6.2.1+dfsg1-1.1 [508 kB] Get:118 http://localhost:3142/debian sid/main armel libnettle8 armel 3.8.1-2 [294 kB] Get:119 http://localhost:3142/debian sid/main armel libhogweed6 armel 3.8.1-2 [315 kB] Get:120 http://localhost:3142/debian sid/main armel libffi8 armel 3.4.4-1 [19.3 kB] Get:121 http://localhost:3142/debian sid/main armel libp11-kit0 armel 0.24.1-1 [328 kB] Get:122 http://localhost:3142/debian sid/main armel libtasn1-6 armel 4.19.0-2 [50.9 kB] Get:123 http://localhost:3142/debian sid/main armel libgnutls30 armel 3.7.8-4 [1294 kB] Get:124 http://localhost:3142/debian sid/main armel libdb5.3 armel 5.3.28+dfsg1-0.10 [572 kB] Get:125 http://localhost:3142/debian sid/main armel libsasl2-modules-db armel 2.1.28+dfsg-10 [19.1 kB] Get:126 http://localhost:3142/debian sid/main armel libsasl2-2 armel 2.1.28+dfsg-10 [51.8 kB] Get:127 http://localhost:3142/debian sid/main armel libldap-2.5-0 armel 2.5.13+dfsg-2+b1 [157 kB] Get:128 http://localhost:3142/debian sid/main armel libnghttp2-14 armel 1.50.0-1+b1 [62.9 kB] Get:129 http://localhost:3142/debian sid/main armel libpsl5 armel 0.21.0-1.2 [56.2 kB] Get:130 http://localhost:3142/debian sid/main armel zlib1g armel 1:1.2.13.dfsg-1 [73.6 kB] Get:131 http://localhost:3142/debian sid/main armel librtmp1 armel 2.4+20151223.gitfa8646d.1-2+b2 [55.1 kB] Get:132 http://localhost:3142/debian sid/main armel libssh2-1 armel 1.10.0-3+b1 [161 kB] Get:133 http://localhost:3142/debian sid/main armel libzstd1 armel 1.5.2+dfsg-1 [237 kB] Get:134 http://localhost:3142/debian sid/main armel libcurl4 armel 7.86.0-2 [322 kB] Get:135 http://localhost:3142/debian sid/main armel libhdf5-103-1 armel 1.10.8+repack-4 [1214 kB] Get:136 http://localhost:3142/debian sid/main armel libhdf5-fortran-102 armel 1.10.8+repack-4 [81.8 kB] Get:137 http://localhost:3142/debian sid/main armel libhdf5-hl-100 armel 1.10.8+repack-4 [65.3 kB] Get:138 http://localhost:3142/debian sid/main armel libhdf5-hl-fortran-100 armel 1.10.8+repack-4 [38.7 kB] Get:139 http://localhost:3142/debian sid/main armel libhdf5-cpp-103-1 armel 1.10.8+repack-4 [115 kB] Get:140 http://localhost:3142/debian sid/main armel libhdf5-hl-cpp-100 armel 1.10.8+repack-4 [25.0 kB] Get:141 http://localhost:3142/debian sid/main armel linux-libc-dev armel 6.0.10-2 [1650 kB] Get:142 http://localhost:3142/debian sid/main armel libcrypt1 armel 1:4.4.33-1 [96.0 kB] Get:143 http://localhost:3142/debian sid/main armel libcrypt-dev armel 1:4.4.33-1 [125 kB] Get:144 http://localhost:3142/debian sid/main armel libtirpc3 armel 1.3.3+ds-1 [72.0 kB] Get:145 http://localhost:3142/debian sid/main armel libnsl2 armel 1.3.0-2 [33.0 kB] Get:146 http://localhost:3142/debian sid/main armel libtirpc-dev armel 1.3.3+ds-1 [182 kB] Get:147 http://localhost:3142/debian sid/main armel libnsl-dev armel 1.3.0-2 [61.7 kB] Get:148 http://localhost:3142/debian sid/main armel libc6-dev armel 2.36-6 [1287 kB] Get:149 http://localhost:3142/debian sid/main armel zlib1g-dev armel 1:1.2.13.dfsg-1 [902 kB] Get:150 http://localhost:3142/debian sid/main armel libjpeg62-turbo armel 1:2.1.2-1+b1 [148 kB] Get:151 http://localhost:3142/debian sid/main armel libjpeg62-turbo-dev armel 1:2.1.2-1+b1 [264 kB] Get:152 http://localhost:3142/debian sid/main armel libjpeg-dev armel 1:2.1.2-1+b1 [75.0 kB] Get:153 http://localhost:3142/debian sid/main armel libcurl4-openssl-dev armel 7.86.0-2 [425 kB] Get:154 http://localhost:3142/debian sid/main armel libssl-dev armel 3.0.7-1 [2101 kB] Get:155 http://localhost:3142/debian sid/main armel libhdf5-dev armel 1.10.8+repack-4 [2616 kB] Get:156 http://localhost:3142/debian sid/main armel libsuperlu-dev armel 5.3.0+dfsg1-2+b1 [22.4 kB] Get:157 http://localhost:3142/debian sid/main armel libarmadillo-dev armel 1:11.4.2+dfsg-1 [403 kB] Get:158 http://localhost:3142/debian sid/main armel libasan8 armel 12.2.0-9 [2092 kB] Get:159 http://localhost:3142/debian sid/main armel libbamtools2.5.2 armel 2.5.2+dfsg-3 [124 kB] Get:160 http://localhost:3142/debian sid/main armel libbamtools-dev armel 2.5.2+dfsg-3 [194 kB] Get:161 http://localhost:3142/debian sid/main armel libgomp1 armel 12.2.0-9 [99.6 kB] Get:162 http://localhost:3142/debian sid/main armel libubsan1 armel 12.2.0-9 [863 kB] Get:163 http://localhost:3142/debian sid/main armel libgcc-12-dev armel 12.2.0-9 [734 kB] Get:164 http://localhost:3142/debian sid/main armel libstdc++-12-dev armel 12.2.0-9 [2083 kB] Get:165 http://localhost:3142/debian sid/main armel libboost1.74-dev armel 1.74.0-17+b2 [9510 kB] Get:166 http://localhost:3142/debian sid/main armel libboost-math1.74.0 armel 1.74.0-17+b2 [395 kB] Get:167 http://localhost:3142/debian sid/main armel libboost-math1.74-dev armel 1.74.0-17+b2 [437 kB] Get:168 http://localhost:3142/debian sid/main armel libboost-math-dev armel 1.74.0.3 [4532 B] Get:169 http://localhost:3142/debian sid/main armel libdisorder0 armel 0.0.2+git20130809.8062ee1-4+b1 [6660 B] Get:170 http://localhost:3142/debian sid/main armel libdisorder-dev armel 0.0.2+git20130809.8062ee1-4+b1 [4840 B] Get:171 http://localhost:3142/debian sid/main armel libjsoncpp25 armel 1.9.5-4 [66.2 kB] Get:172 http://localhost:3142/debian sid/main armel libjsoncpp-dev armel 1.9.5-4 [26.4 kB] Get:173 http://localhost:3142/debian sid/main armel libsmithwaterman0 armel 0.0+git20160702.2610e25-12+b1 [32.3 kB] Get:174 http://localhost:3142/debian sid/main armel libsmithwaterman-dev armel 0.0+git20160702.2610e25-12+b1 [38.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 129 MB in 2s (57.5 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 15686 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-4+b3_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../001-libncurses6_6.3+20220423-2_amd64.deb ... Unpacking libncurses6:amd64 (6.3+20220423-2) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../002-libncursesw6_6.3+20220423-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.3+20220423-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../003-libprocps8_2%3a3.3.17-7.1_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-7.1) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a3.3.17-7.1_amd64.deb ... Unpacking procps (2:3.3.17-7.1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../006-libmagic-mgc_1%3a5.41-4_amd64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../007-libmagic1_1%3a5.41-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.41-4) ... Selecting previously unselected package file. Preparing to unpack .../008-file_1%3a5.41-4_amd64.deb ... Unpacking file (1:5.41-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../009-gettext-base_0.21-10_amd64.deb ... Unpacking gettext-base (0.21-10) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../010-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../011-groff-base_1.22.4-9_amd64.deb ... Unpacking groff-base (1.22.4-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.38.1-4_amd64.deb ... Unpacking bsdextrautils (2.38.1-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../013-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../014-man-db_2.11.1-1_amd64.deb ... Unpacking man-db (2.11.1-1) ... Selecting previously unselected package ucf. Preparing to unpack .../015-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-1_amd64.deb ... Unpacking m4 (1.4.19-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.21-10_all.deb ... Unpacking autopoint (0.21-10) ... Selecting previously unselected package binutils-arm-linux-gnueabi. Preparing to unpack .../021-binutils-arm-linux-gnueabi_2.39-8_amd64.deb ... Unpacking binutils-arm-linux-gnueabi (2.39-8) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../022-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../023-libxml2_2.9.14+dfsg-1.1+b2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b2) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../024-libarchive13_3.6.0-1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.0-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../025-libbrotli1_1.0.9-2+b5_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b5) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../026-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../027-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../028-libldap-2.5-0_2.5.13+dfsg-2+b1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-2+b1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../029-libnghttp2-14_1.50.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.50.0-1+b1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../030-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../031-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../032-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../033-libcurl4_7.86.0-2_amd64.deb ... Unpacking libcurl4:amd64 (7.86.0-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../034-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../035-libjsoncpp25_1.9.5-4_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../036-librhash0_1.4.3-3_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../037-libuv1_1.44.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../038-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../039-cmake_3.25.1-1_amd64.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package gcc-12-arm-linux-gnueabi-base:amd64. Preparing to unpack .../040-gcc-12-arm-linux-gnueabi-base_12.2.0-9cross2_amd64.deb ... Unpacking gcc-12-arm-linux-gnueabi-base:amd64 (12.2.0-9cross2) ... Selecting previously unselected package cpp-12-arm-linux-gnueabi. Preparing to unpack .../041-cpp-12-arm-linux-gnueabi_12.2.0-9cross2_amd64.deb ... Unpacking cpp-12-arm-linux-gnueabi (12.2.0-9cross2) ... Selecting previously unselected package cpp-arm-linux-gnueabi. Preparing to unpack .../042-cpp-arm-linux-gnueabi_4%3a12.2.0-1_amd64.deb ... Unpacking cpp-arm-linux-gnueabi (4:12.2.0-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../043-cross-config_2.6.19_all.deb ... Unpacking cross-config (2.6.19) ... Selecting previously unselected package gcc-12-cross-base. Preparing to unpack .../044-gcc-12-cross-base_12.2.0-9cross2_all.deb ... Unpacking gcc-12-cross-base (12.2.0-9cross2) ... Selecting previously unselected package libc6-armel-cross. Preparing to unpack .../045-libc6-armel-cross_2.36-3cross1_all.deb ... Unpacking libc6-armel-cross (2.36-3cross1) ... Selecting previously unselected package libgcc-s1-armel-cross. Preparing to unpack .../046-libgcc-s1-armel-cross_12.2.0-9cross2_all.deb ... Unpacking libgcc-s1-armel-cross (12.2.0-9cross2) ... Selecting previously unselected package libgomp1-armel-cross. Preparing to unpack .../047-libgomp1-armel-cross_12.2.0-9cross2_all.deb ... Unpacking libgomp1-armel-cross (12.2.0-9cross2) ... Selecting previously unselected package libatomic1-armel-cross. Preparing to unpack .../048-libatomic1-armel-cross_12.2.0-9cross2_all.deb ... Unpacking libatomic1-armel-cross (12.2.0-9cross2) ... Selecting previously unselected package libasan8-armel-cross. Preparing to unpack .../049-libasan8-armel-cross_12.2.0-9cross2_all.deb ... Unpacking libasan8-armel-cross (12.2.0-9cross2) ... Selecting previously unselected package libstdc++6-armel-cross. Preparing to unpack .../050-libstdc++6-armel-cross_12.2.0-9cross2_all.deb ... Unpacking libstdc++6-armel-cross (12.2.0-9cross2) ... Selecting previously unselected package libubsan1-armel-cross. Preparing to unpack .../051-libubsan1-armel-cross_12.2.0-9cross2_all.deb ... 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Selecting previously unselected package libtirpc3:armel. Preparing to unpack .../142-libtirpc3_1.3.3+ds-1_armel.deb ... Unpacking libtirpc3:armel (1.3.3+ds-1) ... Selecting previously unselected package libnsl2:armel. Preparing to unpack .../143-libnsl2_1.3.0-2_armel.deb ... Unpacking libnsl2:armel (1.3.0-2) ... Selecting previously unselected package libtirpc-dev:armel. Preparing to unpack .../144-libtirpc-dev_1.3.3+ds-1_armel.deb ... Unpacking libtirpc-dev:armel (1.3.3+ds-1) ... Selecting previously unselected package libnsl-dev:armel. Preparing to unpack .../145-libnsl-dev_1.3.0-2_armel.deb ... Unpacking libnsl-dev:armel (1.3.0-2) ... Selecting previously unselected package libc6-dev:armel. Preparing to unpack .../146-libc6-dev_2.36-6_armel.deb ... Unpacking libc6-dev:armel (2.36-6) ... Selecting previously unselected package zlib1g-dev:armel. Preparing to unpack .../147-zlib1g-dev_1%3a1.2.13.dfsg-1_armel.deb ... Unpacking zlib1g-dev:armel (1:1.2.13.dfsg-1) ... 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Preparing to unpack .../153-libhdf5-dev_1.10.8+repack-4_armel.deb ... Unpacking libhdf5-dev:armel (1.10.8+repack-4) ... Selecting previously unselected package libsuperlu-dev:armel. Preparing to unpack .../154-libsuperlu-dev_5.3.0+dfsg1-2+b1_armel.deb ... Unpacking libsuperlu-dev:armel (5.3.0+dfsg1-2+b1) ... Selecting previously unselected package libarmadillo-dev:armel. Preparing to unpack .../155-libarmadillo-dev_1%3a11.4.2+dfsg-1_armel.deb ... Unpacking libarmadillo-dev:armel (1:11.4.2+dfsg-1) ... Selecting previously unselected package libasan8:armel. Preparing to unpack .../156-libasan8_12.2.0-9_armel.deb ... Unpacking libasan8:armel (12.2.0-9) ... Selecting previously unselected package libbamtools2.5.2:armel. Preparing to unpack .../157-libbamtools2.5.2_2.5.2+dfsg-3_armel.deb ... Unpacking libbamtools2.5.2:armel (2.5.2+dfsg-3) ... Selecting previously unselected package libbamtools-dev:armel. Preparing to unpack .../158-libbamtools-dev_2.5.2+dfsg-3_armel.deb ... 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Selecting previously unselected package libjsoncpp25:armel. Preparing to unpack .../169-libjsoncpp25_1.9.5-4_armel.deb ... Unpacking libjsoncpp25:armel (1.9.5-4) ... Selecting previously unselected package libjsoncpp-dev:armel. Preparing to unpack .../170-libjsoncpp-dev_1.9.5-4_armel.deb ... Unpacking libjsoncpp-dev:armel (1.9.5-4) ... Selecting previously unselected package libsmithwaterman0:armel. Preparing to unpack .../171-libsmithwaterman0_0.0+git20160702.2610e25-12+b1_armel.deb ... Unpacking libsmithwaterman0:armel (0.0+git20160702.2610e25-12+b1) ... Selecting previously unselected package libsmithwaterman-dev:armel. Preparing to unpack .../172-libsmithwaterman-dev_0.0+git20160702.2610e25-12+b1_armel.deb ... Unpacking libsmithwaterman-dev:armel (0.0+git20160702.2610e25-12+b1) ... Selecting previously unselected package sbuild-build-depends-main-dummy:armel. Preparing to unpack .../173-sbuild-build-depends-main-dummy_0.invalid.0_armel.deb ... Unpacking sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-1) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up binutils-arm-linux-gnueabi (2.39-8) ... Setting up libicu72:amd64 (72.1-3) ... Setting up gcc-12-cross-base (12.2.0-9cross2) ... Setting up bsdextrautils (2.38.1-4) ... Setting up hdf5-helpers:armel (1.10.8+repack-4) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.1) ... Setting up libbrotli1:amd64 (1.0.9-2+b5) ... Setting up libnghttp2-14:amd64 (1.50.0-1+b1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up linux-libc-dev:armel (6.0.10-2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-10) ... Setting up m4 (1.4.19-1) ... Setting up file (1:5.41-4) ... Setting up libyaml-perl (1.30-2) ... Setting up linux-libc-dev-armel-cross (6.0.6-2cross1) ... Setting up gcc-12-base:armel (12.2.0-9) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.19) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.3+20220423-2) ... Setting up autopoint (0.21-10) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up libncursesw6:amd64 (6.3+20220423-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-2) ... Setting up libc6-armel-cross (2.36-3cross1) ... Setting up sensible-utils (0.0.17) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up gcc-12-arm-linux-gnueabi-base:amd64 (12.2.0-9cross2) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libc6-dev-armel-cross (2.36-3cross1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libelf1:amd64 (0.188-1) ... Setting up cpp-12-arm-linux-gnueabi (12.2.0-9cross2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b2) ... Setting up liblocale-gettext-perl (1.07-4+b3) ... Setting up libprocps8:amd64 (2:3.3.17-7.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.0-2) ... Setting up gettext (0.21-10) ... Setting up libgomp1-armel-cross (12.2.0-9cross2) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:amd64 (3.6.0-1) ... Setting up libgcc-s1-armel-cross (12.2.0-9cross2) ... Setting up libstdc++6-armel-cross (12.2.0-9cross2) ... Setting up libatomic1-armel-cross (12.2.0-9cross2) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-2+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up cpp-arm-linux-gnueabi (4:12.2.0-1) ... Setting up libubsan1-armel-cross (12.2.0-9cross2) ... Setting up ucf (3.0043) ... Setting up dh-strip-nondeterminism (1.13.0-2) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-9) ... Setting up procps (2:3.3.17-7.1) ... Setting up libcurl4:amd64 (7.86.0-2) ... Setting up libasan8-armel-cross (12.2.0-9cross2) ... Setting up libgcc-12-dev-armel-cross (12.2.0-9cross2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-12-arm-linux-gnueabi (12.2.0-9cross2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+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 gcc-arm-linux-gnueabi (4:12.2.0-1) ... Setting up cmake (3.25.1-1) ... Setting up libstdc++-12-dev-armel-cross (12.2.0-9cross2) ... Setting up debhelper (13.11.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-12-arm-linux-gnueabi (12.2.0-9cross2) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-arm-linux-gnueabi (4:12.2.0-1) ... Setting up libdebian-dpkgcross-perl (2.6.19) ... Setting up dpkg-cross (2.6.19) ... Setting up crossbuild-essential-armel (12.9) ... Setting up libgcc-s1:armel (12.2.0-9) ... Setting up libc6:armel (2.36-6) ... Setting up libffi8:armel (3.4.4-1) ... Setting up libasan8:armel (12.2.0-9) ... Setting up libtasn1-6:armel (4.19.0-2) ... Setting up libdb5.3:armel (5.3.28+dfsg1-0.10) ... Setting up libstdc++6:armel (12.2.0-9) ... Setting up libdisorder0:armel (0.0.2+git20130809.8062ee1-4+b1) ... Setting up libzstd1:armel (1.5.2+dfsg-1) ... Setting up libkeyutils1:armel (1.6.3-1) ... Setting up libbrotli1:armel (1.0.9-2+b5) ... Setting up libsmithwaterman0:armel (0.0+git20160702.2610e25-12+b1) ... Setting up libnghttp2-14:armel (1.50.0-1+b1) ... Setting up libunistring2:armel (1.0-2) ... Setting up zlib1g:armel (1:1.2.13.dfsg-1) ... Setting up libcrypt1:armel (1:4.4.33-1) ... Setting up libidn2-0:armel (2.3.3-1+b1) ... Setting up libcom-err2:armel (1.46.6~rc1-1+b1) ... Setting up libgomp1:armel (12.2.0-9) ... Setting up libaec0:armel (1.0.6-1+b1) ... Setting up libkrb5support0:armel (1.20.1-1) ... Setting up libsasl2-modules-db:armel (2.1.28+dfsg-10) ... Setting up libblas3:armel (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabi/libblas.so.3 (libblas.so.3-arm-linux-gnueabi) in auto mode Setting up libjpeg62-turbo:armel (1:2.1.2-1+b1) ... Setting up libnettle8:armel (3.8.1-2) ... Setting up libgmp10:armel (2:6.2.1+dfsg1-1.1) ... Setting up libp11-kit0:armel (0.24.1-1) ... Setting up libatomic1:armel (12.2.0-9) ... Setting up libjsoncpp25:armel (1.9.5-4) ... Setting up libk5crypto3:armel (1.20.1-1) ... Setting up libdisorder-dev:armel (0.0.2+git20130809.8062ee1-4+b1) ... Setting up libbamtools2.5.2:armel (2.5.2+dfsg-3) ... Setting up libsasl2-2:armel (2.1.28+dfsg-10) ... Setting up libgfortran5:armel (12.2.0-9) ... Setting up libboost-math1.74.0:armel (1.74.0-17+b2) ... Setting up libubsan1:armel (12.2.0-9) ... Setting up libcrypt-dev:armel (1:4.4.33-1) ... Setting up libblas-dev:armel (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/blas/libblas.so to provide /usr/lib/arm-linux-gnueabi/libblas.so (libblas.so-arm-linux-gnueabi) in auto mode Setting up libsz2:armel (1.0.6-1+b1) ... Setting up libjsoncpp-dev:armel (1.9.5-4) ... Setting up liblapack3:armel (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabi/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabi) in auto mode Setting up libpsl5:armel (0.21.0-1.2) ... Setting up libhogweed6:armel (3.8.1-2) ... Setting up libaec-dev:armel (1.0.6-1+b1) ... Setting up libarpack2:armel (3.8.0-3) ... Setting up libssl3:armel (3.0.7-1) ... Setting up libsuperlu5:armel (5.3.0+dfsg1-2+b1) ... Setting up libgnutls30:armel (3.7.8-4) ... Setting up librtmp1:armel (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libgcc-12-dev:armel (12.2.0-9) ... Setting up libssl-dev:armel (3.0.7-1) ... Setting up liblapack-dev:armel (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabi/liblapack.so (liblapack.so-arm-linux-gnueabi) in auto mode Setting up libsmithwaterman-dev:armel (0.0+git20160702.2610e25-12+b1) ... Setting up libssh2-1:armel (1.10.0-3+b1) ... Setting up libkrb5-3:armel (1.20.1-1) ... Setting up libsuperlu-dev:armel (5.3.0+dfsg1-2+b1) ... Setting up libarpack2-dev:armel (3.8.0-3) ... Setting up libarmadillo11:armel (1:11.4.2+dfsg-1) ... Setting up libldap-2.5-0:armel (2.5.13+dfsg-2+b1) ... Setting up libgssapi-krb5-2:armel (1.20.1-1) ... Setting up libcurl4:armel (7.86.0-2) ... Setting up libtirpc3:armel (1.3.3+ds-1) ... Setting up libtirpc-dev:armel (1.3.3+ds-1) ... Setting up libcurl4-openssl-dev:armel (7.86.0-2) ... Setting up libhdf5-103-1:armel (1.10.8+repack-4) ... Setting up libnsl2:armel (1.3.0-2) ... Setting up libhdf5-cpp-103-1:armel (1.10.8+repack-4) ... Setting up libhdf5-hl-100:armel (1.10.8+repack-4) ... Setting up libhdf5-hl-cpp-100:armel (1.10.8+repack-4) ... Setting up libhdf5-fortran-102:armel (1.10.8+repack-4) ... Setting up libnsl-dev:armel (1.3.0-2) ... Setting up libhdf5-hl-fortran-100:armel (1.10.8+repack-4) ... Setting up libc6-dev:armel (2.36-6) ... Setting up libstdc++-12-dev:armel (12.2.0-9) ... Setting up libjpeg62-turbo-dev:armel (1:2.1.2-1+b1) ... Setting up zlib1g-dev:armel (1:1.2.13.dfsg-1) ... Setting up libboost1.74-dev:armel (1.74.0-17+b2) ... Setting up libjpeg-dev:armel (1:2.1.2-1+b1) ... Setting up libbamtools-dev:armel (2.5.2+dfsg-3) ... Setting up libhdf5-dev:armel (1.10.8+repack-4) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabi/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libboost-math1.74-dev:armel (1.74.0-17+b2) ... Setting up libboost-math-dev:armel (1.74.0.3) ... Setting up libarmadillo-dev:armel (1:11.4.2+dfsg-1) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.36-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) amd64 (x86_64) Toolchain package versions: binutils_2.39-8 dpkg-dev_1.21.11 g++-11_11.3.0-8 g++-12_12.2.0-9 gcc-11_11.3.0-8 gcc-12_12.2.0-9 libc6-dev_2.36-6 libstdc++-11-dev_11.3.0-8 libstdc++-12-dev_12.2.0-9 libstdc++-12-dev-armel-cross_12.2.0-9cross2 libstdc++6_12.2.0-9 libstdc++6-armel-cross_12.2.0-9cross2 linux-libc-dev_6.0.10-2 Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3 base-passwd_3.6.1 bash_5.2-2+b1 binutils_2.39-8 binutils-arm-linux-gnueabi_2.39-8 binutils-common_2.39-8 binutils-x86-64-linux-gnu_2.39-8 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b1 cmake_3.25.1-1 cmake-data_3.25.1-1 coreutils_9.1-1 cpp_4:12.2.0-1 cpp-11_11.3.0-8 cpp-12_12.2.0-9 cpp-12-arm-linux-gnueabi_12.2.0-9cross2 cpp-arm-linux-gnueabi_4:12.2.0-1 cross-config_2.6.19 crossbuild-essential-armel_12.9 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.1 debian-archive-keyring_2021.1.1 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dpkg_1.21.11 dpkg-cross_2.6.19 dpkg-dev_1.21.11 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1+b1 fakeroot_1.30.1-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1 g++-11_11.3.0-8 g++-12_12.2.0-9 g++-12-arm-linux-gnueabi_12.2.0-9cross2 g++-arm-linux-gnueabi_4:12.2.0-1 gcc_4:12.2.0-1 gcc-11_11.3.0-8 gcc-11-base_11.3.0-8 gcc-12_12.2.0-9 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tvc Binary: tvc Architecture: any Version: 5.0.3+git20151221.80e144e+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Dominique Belhachemi , Andreas Tille Homepage: http://ioncommunity.thermofisher.com Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), 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 7d0306db9bc6dc0e7cd4dede9e0a4fc26451cb66 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz Checksums-Sha256: 3339f118d2fe983bc028630d5bf5238b6e91b70a85e8046a742588a6c342740c 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz ea878d69c94a1606583404cf23717d6a1dcc537bc4e6bd2c559ad2650939a52f 9800 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dpkg-source: info: applying sse.patch dpkg-source: info: applying use_debian_packaged_smithwaterman.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying gcc11.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-bb3bf4b6-72f7-4375-9080-e21747b56759 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Mohammed Bilal dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-arm-linux-gnueabi && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" 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CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/arm-linux-gnueabi-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/arm-linux-gnueabi-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_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE QMAKE_EXECUTABLE -- Build files have been written to: /<>/obj-arm-linux-gnueabi dh_auto_build -a cd obj-arm-linux-gnueabi && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-arm-linux-gnueabi' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabi/CMakeFiles /<>/obj-arm-linux-gnueabi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-arm-linux-gnueabi' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' cd /<>/obj-arm-linux-gnueabi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi /<>/obj-arm-linux-gnueabi/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabi' [ 1%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /<>/VariantCaller/VariantCaller.cpp /<>/VariantCaller/VariantCaller.cpp: In function ‘void TheSilenceOfTheArmadillos(std::ofstream&)’: /<>/VariantCaller/VariantCaller.cpp:36:24: 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:385, from /<>/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /<>/VariantCaller/VariantCaller.cpp:37:24: warning: ‘void arma::set_stream_err2(std::ostream&)’ is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/armadillo_bits/debug.hpp:103:1: note: declared here 103 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ [ 3%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o -c /<>/VariantCaller/BAMWalkerEngine.cpp [ 4%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -c /<>/VariantCaller/OrderedBAMWriter.cpp [ 6%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /<>/VariantCaller/SampleManager.cpp [ 7%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /<>/VariantCaller/TargetsManager.cpp [ 9%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /<>/VariantCaller/HandleVariant.cpp [ 10%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /<>/VariantCaller/HotspotReader.cpp [ 12%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /<>/VariantCaller/MetricsManager.cpp [ 14%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /<>/VariantCaller/Bookkeeping/MiscUtil.cpp [ 15%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -c /<>/VariantCaller/Bookkeeping/ExtendParameters.cpp [ 17%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /<>/VariantCaller/Bookkeeping/InputStructures.cpp In file included from /usr/arm-linux-gnueabi/include/c++/12/map:60, from /<>/VariantCaller/Bookkeeping/InputStructures.h:14, from /<>/VariantCaller/Bookkeeping/InputStructures.cpp:7: /usr/arm-linux-gnueabi/include/c++/12/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, LinearCalibrationModel>}; _Key = std::__cxx11::basic_string; _Val = std::pair, LinearCalibrationModel>; _KeyOfValue = std::_Select1st, LinearCalibrationModel> >; _Compare = std::less >; _Alloc = std::allocator, LinearCalibrationModel> >]’: /usr/arm-linux-gnueabi/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, LinearCalibrationModel>, std::_Select1st, LinearCalibrationModel> >, std::less >, std::allocator, LinearCalibrationModel> > >::const_iterator’ changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/12/vector:70, from /<>/VariantCaller/Bookkeeping/InputStructures.h:12: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const DPTreephaser&}; _Tp = DPTreephaser; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/12/vector:64: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = DPTreephaser; _Alloc = std::allocator]’, inlined from ‘PersistingThreadObjects::PersistingThreadObjects(const InputStructures&)’ at /<>/VariantCaller/Bookkeeping/InputStructures.cpp:323:38: /usr/arm-linux-gnueabi/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/12/map:61: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair, std::allocator >, LinearCalibrationModel>}; _Key = std::__cxx11::basic_string; _Tp = LinearCalibrationModel; _Compare = std::less >; _Alloc = std::allocator, LinearCalibrationModel> >]’, inlined from ‘std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair, LinearCalibrationModel>; _Key = std::__cxx11::basic_string; _Tp = LinearCalibrationModel; _Compare = std::less >; _Alloc = std::allocator, LinearCalibrationModel> >]’ at /usr/arm-linux-gnueabi/include/c++/12/bits/stl_map.h:858:27, inlined from ‘void RecalibrationHandler::ReadRecalibrationFromComments(const BamTools::SamHeader&, const std::map, int>&)’ at /<>/VariantCaller/Bookkeeping/InputStructures.cpp:272:36: /usr/arm-linux-gnueabi/include/c++/12/bits/stl_map.h:638:45: note: parameter passing for argument of type ‘std::map, LinearCalibrationModel>::const_iterator’ {aka ‘std::_Rb_tree, std::pair, LinearCalibrationModel>, std::_Select1st, LinearCalibrationModel> >, std::less >, std::allocator, LinearCalibrationModel> > >::const_iterator’} changed in GCC 7.1 638 | return _M_t._M_emplace_hint_unique(__pos, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 639 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -c /<>/VariantCaller/Bookkeeping/VcfFormat.cpp [ 20%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /<>/VariantCaller/Reads/ExtendedReadInfo.cpp [ 21%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /<>/VariantCaller/Splice/ErrorMotifs.cpp [ 23%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /<>/VariantCaller/Splice/LocalContext.cpp [ 25%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -c /<>/VariantCaller/Splice/ClassifyVariant.cpp [ 26%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -c /<>/VariantCaller/Splice/SpliceVariantHypotheses.cpp [ 28%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o -c /<>/VariantCaller/Filter/DecisionTreeData.cpp [ 29%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o.d -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 [ 31%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -c /<>/VariantCaller/HypothesisEvaluator.cpp [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -c /<>/VariantCaller/EnsembleEval/DiagnosticJSON.cpp [ 34%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -c /<>/VariantCaller/EnsembleEval/BiasGenerator.cpp [ 35%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -c /<>/VariantCaller/EnsembleEval/SigmaGenerator.cpp [ 37%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -c /<>/VariantCaller/EnsembleEval/SkewGenerator.cpp [ 39%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -c /<>/VariantCaller/EnsembleEval/PosteriorInference.cpp [ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -c /<>/VariantCaller/EnsembleEval/ShortStack.cpp [ 42%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -c /<>/VariantCaller/EnsembleEval/StackEngine.cpp [ 43%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -c /<>/VariantCaller/EnsembleEval/CrossHypotheses.cpp [ 45%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -c /<>/external/vcflib/Variant.cpp [ 46%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /<>/external/vcflib/split.cpp [ 48%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<>/external/vcflib/tabixpp/tabix.cpp [ 50%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o /usr/bin/arm-linux-gnueabi-gcc -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o.d -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:336:42: 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; | ^~~~~~~~ [ 51%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/arm-linux-gnueabi-gcc -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o.d -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:678:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 53%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -MF CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o.d -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /<>/external/freebayes/src/AlleleParser.cpp [ 54%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /<>/BaseCaller/PIDloop.cpp [ 56%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -c /<>/BaseCaller/DPTreephaser.cpp [ 57%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -MF CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o.d -o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -c /<>/Calibration/LinearCalibrationModel.cpp [ 59%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -MF CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o.d -o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o -c /<>/Calibration/FlowAlignment.cpp [ 60%] Building CXX object CMakeFiles/tvc.dir/Util/OptArgs.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD 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[with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) 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[with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/arm-linux-gnueabi/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘void OptArgs::StringToDoubleVector(std::vector&, const std::string&, const std::string&, char)’ at /<>/Util/OptArgs.cpp:474:21: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 76%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval 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-I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o -c /<>/VariantCaller/tvcutils/prepare_hotspots.cpp [ 84%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. 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-MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /<>/VariantCaller/tvcutils/unify_vcf.cpp In file included from /<>/VariantCaller/tvcutils/viterbi.h:64, from /<>/VariantCaller/tvcutils/unify_vcf.cpp:19: /<>/VariantCaller/tvcutils/viterbi.hpp: In instantiation of ‘void markov_chain::optimal_path() [with T = unsigned int]’: /<>/VariantCaller/tvcutils/viterbi.hpp:64:3: required from ‘void markov_chain::initialize(_ForwardIterator, _ForwardIterator, T, T) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]’ /<>/VariantCaller/tvcutils/viterbi.hpp:38:13: required from ‘markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]’ /<>/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here /<>/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of ‘constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >]’, declared with attribute ‘nodiscard’ [-Wunused-result] 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { | ~~~^~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/12/string:47, from /<>/VariantCaller/tvcutils/unify_vcf.cpp:7: /usr/arm-linux-gnueabi/include/c++/12/bits/stl_iterator.h:458:5: note: declared here 458 | operator!=(const reverse_iterator<_Iterator>& __x, | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/12/vector:70, from /<>/VariantCaller/tvcutils/unify_vcf.cpp:13: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {markov_state}; _Tp = markov_state; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = markov_state; _Alloc = std::allocator]’ at /usr/arm-linux-gnueabi/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘void markov_chain::generate_states(T, T) [with T = unsigned int]’ at /<>/VariantCaller/tvcutils/viterbi.hpp:78:21: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -c /<>/VariantCaller/TargetsManager.cpp [ 89%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -c /<>/Util/OptArgs.cpp In file included from /usr/arm-linux-gnueabi/include/c++/12/vector:70, from /<>/Util/OptArgs.h:11, from /<>/Util/OptArgs.cpp:4: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/arm-linux-gnueabi/include/c++/12/bits/stl_vector.h:1294:21, inlined from ‘void OptArgs::StringToDoubleVector(std::vector&, const std::string&, const std::string&, char)’ at /<>/Util/OptArgs.cpp:474:21: /usr/arm-linux-gnueabi/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /<>/external/vcflib/Variant.cpp [ 92%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /<>/external/vcflib/split.cpp [ 93%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<>/external/vcflib/tabixpp/tabix.cpp [ 95%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/arm-linux-gnueabi-gcc -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /<>/external/vcflib/tabixpp/index.c /<>/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’: /<>/external/vcflib/tabixpp/index.c:336:42: 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; | ^~~~~~~~ [ 96%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/arm-linux-gnueabi-gcc -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -I/<>/VariantCaller/EnsembleEval -I/<>/VariantCaller/Bookkeeping -I/<>/VariantCaller/Reads -I/<>/VariantCaller/Splice -I/<>/VariantCaller/Filter -I/<>/realignment -I/<>/file-io -I/<>/BaseCaller -I/<>/Calibration -I/<>/Util -I/<> -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /<>/external/vcflib/tabixpp/bgzf.c /<>/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’: /<>/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o /usr/bin/arm-linux-gnueabi-g++ -DALIGNSTATS_IGNORE -I/<>/external/vcflib -I/<>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<>/VariantCaller -I/<>/VariantCaller/FlowDistEval -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 -MD -MT CMakeFiles/tvcutils.dir/IonVersion.cpp.o -MF CMakeFiles/tvcutils.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /<>/obj-arm-linux-gnueabi/IonVersion.cpp [100%] Linking CXX executable tvcutils /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1 /usr/bin/arm-linux-gnueabi-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/<>/obj-arm-linux-gnueabi' [100%] Built target tvcutils make[2]: Leaving directory '/<>/obj-arm-linux-gnueabi' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabi/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-arm-linux-gnueabi' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/tvc/ -a cd obj-arm-linux-gnueabi && make -j1 install DESTDIR=/<>/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-arm-linux-gnueabi' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-arm-linux-gnueabi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-arm-linux-gnueabi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tvc/usr/bin/tvc -- Installing: /<>/debian/tvc/usr/bin/tvcassembly -- Installing: /<>/debian/tvc/usr/bin/tvcutils -- Installing: /<>/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /<>/debian/tvc/usr/share/TVC/sse -- Installing: /<>/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /<>/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /<>/debian/tvc/usr/share/TVC/examples -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /<>/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf make[1]: Leaving directory '/<>/obj-arm-linux-gnueabi' dh_installdocs -a dh_installchangelogs -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcutils contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/tvc/usr/bin/tvcassembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/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-5_armel.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armel.deb'. dpkg-genbuildinfo --build=any -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.buildinfo dpkg-genchanges --build=any -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-12-04T16:56:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.changes: --------------------------------------------------- Format: 1.8 Date: Mon, 05 Sep 2022 17:20:03 +0000 Source: tvc Binary: tvc tvc-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 5.0.3+git20151221.80e144e+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Mohammed Bilal Description: tvc - genetic variant caller for Ion Torrent sequencing platforms Changes: tvc (5.0.3+git20151221.80e144e+dfsg-5) unstable; urgency=medium . * Team upload. * Add autopkgtest * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. Checksums-Sha1: d71f4f27b844b94a7e9547f750803621f701b930 11148476 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armel.deb ba86cbbb0ea9e30bc92fe38ac22004eef8d254e5 7542 tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.buildinfo 78a5c40f583e73326af00f5132652e4bb22acb8c 962432 tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.deb Checksums-Sha256: 38f4129f2c57aaebc11e4d2f460e79e3c772e62ab3704cefb7d0d7120cb260b7 11148476 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armel.deb 7f47be9f3bb64ed7db0851ea289be6d5b56096a92c5f690c19ad034f99a38f77 7542 tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.buildinfo 0109cd5d4810e0c35131b6133ffd4a911703f828962d6ae7c576cff59afc06d1 962432 tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.deb Files: 44ce170904c4132d7387278bbe08027a 11148476 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armel.deb 10b5c82958109bb71456aa5a8c39f35b 7542 science optional tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.buildinfo 39dbbc7c3a7ad4c39f4a67c2d7719460 962432 science optional tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.deb /<>/tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.changes.new could not be renamed to /<>/tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: tvc Binary: tvc tvc-dbgsym Architecture: armel Version: 5.0.3+git20151221.80e144e+dfsg-5 Checksums-Md5: 44ce170904c4132d7387278bbe08027a 11148476 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armel.deb 39dbbc7c3a7ad4c39f4a67c2d7719460 962432 tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.deb Checksums-Sha1: d71f4f27b844b94a7e9547f750803621f701b930 11148476 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armel.deb 78a5c40f583e73326af00f5132652e4bb22acb8c 962432 tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.deb Checksums-Sha256: 38f4129f2c57aaebc11e4d2f460e79e3c772e62ab3704cefb7d0d7120cb260b7 11148476 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armel.deb 0109cd5d4810e0c35131b6133ffd4a911703f828962d6ae7c576cff59afc06d1 962432 tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 04 Dec 2022 16:56:26 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-10), autotools-dev (= 20220109.1), base-files (= 12.3), base-passwd (= 3.6.1), bash (= 5.2-2+b1), binutils (= 2.39-8), binutils-common (= 2.39-8), binutils-x86-64-linux-gnu (= 2.39-8), bsdextrautils (= 2.38.1-4), bsdutils (= 1:2.38.1-4), build-essential (= 12.9), bzip2 (= 1.0.8-5+b1), cmake (= 3.25.1-1), cmake-data (= 3.25.1-1), coreutils (= 9.1-1), cpp (= 4:12.2.0-1), cpp-11 (= 11.3.0-8), cpp-12 (= 12.2.0-9), dash (= 0.5.11+git20210903+057cd650a4ed-9), debconf (= 1.5.80), debhelper (= 13.11.1), debianutils (= 5.7-0.4), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-2), diffutils (= 1:3.8-1), dpkg (= 1.21.11), dpkg-dev (= 1.21.11), dwz (= 0.14+20220924-2), file (= 1:5.41-4), findutils (= 4.9.0-3), g++ (= 4:12.2.0-1), g++-12 (= 12.2.0-9), gcc (= 4:12.2.0-1), gcc-11 (= 11.3.0-8), gcc-11-base (= 11.3.0-8), gcc-12 (= 12.2.0-9), gcc-12-base (= 12.2.0-9), gettext (= 0.21-10), gettext-base (= 0.21-10), grep (= 3.8-3), groff-base (= 1.22.4-9), gzip (= 1.12-1), hdf5-helpers (= 1.10.8+repack-4), hostname (= 3.23), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-2), libaec-dev (= 1.0.6-1+b1), libaec0 (= 1.0.6-1+b1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.6.0-1), libarmadillo-dev (= 1:11.4.2+dfsg-1), libarmadillo11 (= 1:11.4.2+dfsg-1), libarpack2 (= 3.8.0-3), libarpack2-dev (= 3.8.0-3), libasan6 (= 11.3.0-8), libasan8 (= 12.2.0-9), libatomic1 (= 12.2.0-9), libattr1 (= 1:2.5.1-2), libaudit-common (= 1:3.0.7-1.1), libaudit1 (= 1:3.0.7-1.1+b2), libbamtools-dev (= 2.5.2+dfsg-3), libbamtools2.5.2 (= 2.5.2+dfsg-3), libbinutils (= 2.39-8), libblas-dev (= 3.11.0-2), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-4), libboost-math-dev (= 1.74.0.3), libboost-math1.74-dev (= 1.74.0-17+b2), libboost-math1.74.0 (= 1.74.0-17+b2), libboost1.74-dev (= 1.74.0-17+b2), libbrotli1 (= 1.0.9-2+b5), libbz2-1.0 (= 1.0.8-5+b1), libc-bin (= 2.36-6), libc-dev-bin (= 2.36-6), libc6 (= 2.36-6), libc6-dev (= 2.36-6), libcap-ng0 (= 0.8.3-1+b2), libcap2 (= 1:2.44-1), libcc1-0 (= 12.2.0-9), libcom-err2 (= 1.46.6~rc1-1+b1), libcrypt-dev (= 1:4.4.33-1), libcrypt1 (= 1:4.4.33-1), libctf-nobfd0 (= 2.39-8), libctf0 (= 2.39-8), libcurl4 (= 7.86.0-2), libcurl4-openssl-dev (= 7.86.0-2), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.265), libdebhelper-perl (= 13.11.1), libdisorder-dev (= 0.0.2+git20130809.8062ee1-4+b1), libdisorder0 (= 0.0.2+git20130809.8062ee1-4+b1), libdpkg-perl (= 1.21.11), libelf1 (= 0.188-1), libexpat1 (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.0-2), libgcc-11-dev (= 11.3.0-8), libgcc-12-dev (= 12.2.0-9), libgcc-s1 (= 12.2.0-9), libgcrypt20 (= 1.10.1-3), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 12.2.0-9), libgmp10 (= 2:6.2.1+dfsg1-1.1), libgnutls30 (= 3.7.8-4), libgomp1 (= 12.2.0-9), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.39-8), libgssapi-krb5-2 (= 1.20.1-1), libhdf5-103-1 (= 1.10.8+repack-4), libhdf5-cpp-103-1 (= 1.10.8+repack-4), libhdf5-dev (= 1.10.8+repack-4), libhdf5-fortran-102 (= 1.10.8+repack-4), libhdf5-hl-100 (= 1.10.8+repack-4), libhdf5-hl-cpp-100 (= 1.10.8+repack-4), libhdf5-hl-fortran-100 (= 1.10.8+repack-4), libhogweed6 (= 3.8.1-2), libicu72 (= 72.1-3), libidn2-0 (= 2.3.3-1+b1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-9), libjpeg-dev (= 1:2.1.2-1+b1), libjpeg62-turbo (= 1:2.1.2-1+b1), libjpeg62-turbo-dev (= 1:2.1.2-1+b1), libjsoncpp-dev (= 1.9.5-4), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.20.1-1), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.20.1-1), libkrb5support0 (= 1.20.1-1), liblapack-dev (= 3.11.0-2), liblapack3 (= 3.11.0-2), libldap-2.5-0 (= 2.5.13+dfsg-2+b1), liblsan0 (= 12.2.0-9), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.2.9-0.0), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4), libmpc3 (= 1.2.1-2), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.50.0-1+b1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libnumber-compare-perl (= 0.03-3), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.5.2-5), libpam-modules-bin (= 1.5.2-5), libpam-runtime (= 1.5.2-5), libpam0g (= 1.5.2-5), libpcre2-8-0 (= 10.40-3), libperl5.36 (= 5.36.0-4), libpipeline1 (= 1.5.7-1), libprocps8 (= 2:3.3.17-7.1), libpsl5 (= 0.21.0-1.2), libquadmath0 (= 12.2.0-9), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.28+dfsg-10), libsasl2-modules-db (= 2.1.28+dfsg-10), libseccomp2 (= 2.5.4-1+b2), libselinux1 (= 3.4-1+b3), libsmartcols1 (= 2.38.1-4), libsmithwaterman-dev (= 0.0+git20160702.2610e25-12+b1), libsmithwaterman0 (= 0.0+git20160702.2610e25-12+b1), libssh2-1 (= 1.10.0-3+b1), libssl-dev (= 3.0.7-1), libssl3 (= 3.0.7-1), libstdc++-12-dev (= 12.2.0-9), libstdc++6 (= 12.2.0-9), libsub-override-perl (= 0.09-4), libsuperlu-dev (= 5.3.0+dfsg1-2+b1), libsuperlu5 (= 5.3.0+dfsg1-2+b1), libsystemd0 (= 252.2-1), libsz2 (= 1.0.6-1+b1), libtasn1-6 (= 4.19.0-2), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan0 (= 11.3.0-8), libtsan2 (= 12.2.0-9), libubsan1 (= 12.2.0-9), libuchardet0 (= 0.0.7-1), libudev1 (= 252.2-1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4), libuv1 (= 1.44.2-1), libxml2 (= 2.9.14+dfsg-1.1+b2), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 6.0.10-2), login (= 1:4.13+dfsg1-1), m4 (= 1.4.19-1), make (= 4.3-4.1), man-db (= 2.11.1-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7), perl (= 5.36.0-4), perl-base (= 5.36.0-4), perl-modules-5.36 (= 5.36.0-4), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-7.1), rpcsvc-proto (= 1.4.3-1), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.05-7), tar (= 1.34+dfsg-1.1), usrmerge (= 33), util-linux (= 2.38.1-4), util-linux-extra (= 2.38.1-4), xz-utils (= 5.2.9-0.0), zlib1g (= 1:1.2.13.dfsg-1), zlib1g-dev (= 1:1.2.13.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1662398403" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_armel.deb ----------------------------------------------------- new Debian package, version 2.0. size 11148476 bytes: control archive=708 bytes. 488 bytes, 12 lines control 399 bytes, 4 lines md5sums Package: tvc-dbgsym Source: tvc Version: 5.0.3+git20151221.80e144e+dfsg-5 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 11206 Depends: tvc (= 5.0.3+git20151221.80e144e+dfsg-5) Section: debug Priority: optional Description: debug symbols for tvc Build-Ids: 4ee94b91e160f711799f4fc95eadecb6d8e7b6b0 91d63d24d27036a3de00a8ebb4de41173f6f6793 c9148cc946b62183e231b0800c8c8e3abbe7a5ef drwxr-xr-x root/root 0 2022-09-05 17:20 ./ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/lib/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/lib/debug/.build-id/4e/ -rw-r--r-- root/root 7900132 2022-09-05 17:20 ./usr/lib/debug/.build-id/4e/e94b91e160f711799f4fc95eadecb6d8e7b6b0.debug drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/lib/debug/.build-id/91/ -rw-r--r-- root/root 2256504 2022-09-05 17:20 ./usr/lib/debug/.build-id/91/d63d24d27036a3de00a8ebb4de41173f6f6793.debug drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/lib/debug/.build-id/c9/ -rw-r--r-- root/root 825304 2022-09-05 17:20 ./usr/lib/debug/.build-id/c9/148cc946b62183e231b0800c8c8e3abbe7a5ef.debug drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/lib/debug/.dwz/arm-linux-gnueabi/ -rw-r--r-- root/root 477336 2022-09-05 17:20 ./usr/lib/debug/.dwz/arm-linux-gnueabi/tvc.debug drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-09-05 17:20 ./usr/share/doc/tvc-dbgsym -> tvc tvc_5.0.3+git20151221.80e144e+dfsg-5_armel.deb ---------------------------------------------- new Debian package, version 2.0. size 962432 bytes: control archive=1680 bytes. 994 bytes, 16 lines control 2459 bytes, 28 lines md5sums Package: tvc Version: 5.0.3+git20151221.80e144e+dfsg-5 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 3088 Depends: libarmadillo11 (>= 1:11.4.2+dfsg), libbamtools2.5.2 (>= 2.5.2+dfsg), libc6 (>= 2.34), libdisorder0 (>= 0.0.2), libgcc-s1 (>= 3.5), libjsoncpp25 (>= 1.9.5), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 11), 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 2022-09-05 17:20 ./ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/bin/ -rwxr-xr-x root/root 987300 2022-09-05 17:20 ./usr/bin/tvc -rwxr-xr-x root/root 199068 2022-09-05 17:20 ./usr/bin/tvcassembly -rwxr-xr-x root/root 527192 2022-09-05 17:20 ./usr/bin/tvcutils -rwxr-xr-x root/root 12985 2022-09-05 17:20 ./usr/bin/variant_caller_pipeline.py drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/TVC/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/TVC/examples/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/TVC/examples/example1/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./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 2022-09-05 17:20 ./usr/share/TVC/pluginMedia/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./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 2022-09-05 17:20 ./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 2022-09-05 17:20 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/doc/tvc/ -rw-r--r-- root/root 1078 2022-09-05 16:49 ./usr/share/doc/tvc/README.Debian -rw-r--r-- root/root 657 2022-09-05 17:20 ./usr/share/doc/tvc/changelog.Debian.gz -rw-r--r-- root/root 2939 2022-09-05 17:19 ./usr/share/doc/tvc/copyright drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-09-05 17:20 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 135 2022-09-05 16:49 ./usr/share/lintian/overrides/tvc lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [579 B] Get:5 copy:/<>/apt_archive ./ Packages [662 B] Fetched 2204 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:armel t1utils unzip 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 14.0 MB of archives. After this operation, 51.5 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://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.2 [68.5 kB] Get:4 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.7-1 [1400 kB] Get:5 http://localhost:3142/debian sid/main amd64 ca-certificates all 20211016 [156 kB] Get:6 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.64-1 [36.6 kB] Get:7 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB] Get:8 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.2 [165 kB] Get:9 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1 [564 kB] Get:10 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.40.0-1 [838 kB] Get:11 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1 [948 kB] Get:12 http://localhost:3142/debian sid/main amd64 iso-codes all 4.12.0-1 [2888 kB] Get:13 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:14 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB] Get:15 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:16 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:17 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:18 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:19 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:21 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:23 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.63-1+b1 [44.0 kB] Get:24 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:25 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b1 [123 kB] Get:26 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:27 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:28 http://localhost:3142/debian sid/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:29 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get:30 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.80-1 [101 kB] Get:31 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.54-1 [224 kB] Get:32 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:33 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.13-2 [19.4 kB] Get:34 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get:35 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:36 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.28-2 [16.4 kB] Get:37 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:38 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.928-3 [9724 B] Get:39 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:40 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:41 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:42 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.32-1+b1 [130 kB] Get:43 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:44 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:45 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:46 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:47 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.58-2 [43.6 kB] Get:48 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB] Get:49 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:50 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:51 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:52 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:53 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB] Get:54 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:55 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:56 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB] Get:57 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB] Get:58 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:59 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:60 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:61 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:62 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:63 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:64 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:65 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:66 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.10-1 [24.0 kB] Get:69 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:70 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get:71 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:72 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:73 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:74 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:75 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.077-1 [217 kB] Get:76 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get:77 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:78 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:79 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.67-1 [194 kB] Get:80 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:81 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:82 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.023-2 [11.0 kB] Get:83 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:84 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004004-1 [13.3 kB] Get:85 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:86 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.58-3 [36.5 kB] Get:87 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:88 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-4 [42.0 kB] Get:89 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:90 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:91 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:92 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:93 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:94 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005004-3 [60.5 kB] Get:95 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:96 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:97 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB] Get:98 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:99 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB] Get:100 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.26-2+b1 [12.6 kB] Get:101 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:102 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.124-1 [56.1 kB] Get:103 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB] Get:104 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:105 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.634-1+b2 [43.1 kB] Get:106 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:107 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.001+ds-1+b1 [102 kB] Get:108 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.001+ds-2 [105 kB] Get:109 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:110 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.30-1 [57.3 kB] Get:111 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.27-1+b1 [28.8 kB] Get:112 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB] Get:113 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B] Get:114 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.13-2 [12.4 kB] Get:115 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB] Get:116 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:117 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB] Get:118 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-1+b4 [20.0 kB] Get:119 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.15-1 [120 kB] Get:120 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:121 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.84+ds-1+b1 [34.7 kB] Get:122 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-4 [64.0 kB] Get:123 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:124 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:125 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:126 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-27 [172 kB] Get:127 http://localhost:3142/debian sid/main amd64 lintian all 2.115.3 [1417 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.0 MB in 0s (155 MB/s) Selecting previously unselected package netbase. 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Setting up liblz1:amd64 (1.13-4) ... Setting up libberkeleydb-perl:amd64 (0.64-2+b1) ... Setting up plzip (1.10-4) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-1+b4) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.13-2) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:amd64 (4.32-1+b1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-27) ... Setting up libsqlite3-0:amd64 (3.40.0-1) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libyaml-libyaml-perl (0.84+ds-1+b1) ... Setting up libio-interactive-perl (1.023-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:amd64 (2.5.5-5) ... Setting up libconfig-tiny-perl (2.28-2) ... Setting up libsereal-encoder-perl (5.001+ds-2) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.928-3) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004004-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... 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Setting up libpath-tiny-perl (0.124-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-2) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.7-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up readline-common (8.2-1.2) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.001+ds-1+b1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.17-1) ... Setting up iso-codes (4.12.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.30-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libreadline8:amd64 (8.2-1.2) ... Setting up libnet-http-perl (6.22-1) ... Setting up libtext-markdown-discount-perl (0.13-2) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 127 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.80-1) ... Setting up gpgconf (2.2.40-1) ... Setting up libio-socket-ssl-perl (2.077-1) ... Setting up gpg (2.2.40-1) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libhtml-form-perl (6.10-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.54-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.58-2) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-3) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.67-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.15-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up lintian (2.115.3) ... Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.36-6) ... Processing triggers for man-db (2.11.1-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 140068 Build-Time: 170 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 17 Job: tvc_5.0.3+git20151221.80e144e+dfsg-5 Lintian: pass Machine Architecture: amd64 Package: tvc Package-Time: 197 Source-Version: 5.0.3+git20151221.80e144e+dfsg-5 Space: 140068 Status: successful Version: 5.0.3+git20151221.80e144e+dfsg-5 -------------------------------------------------------------------------------- Finished at 2022-12-04T16:56:26Z Build needed 00:03:17, 140068k disk space