sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | berkeley-express 1.5.3+dfsg-2 (armhf) Mon, 18 Oct 2021 04:57:20 +0000 | +==============================================================================+ Package: berkeley-express Version: 1.5.3+dfsg-2 Source Version: 1.5.3+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-fae70d87-c886-4bff-b711-4fdcb773dcb8' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-8Jviad/resolver-vwougX' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [165 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [63.6 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-10-18-0201.36-F-2021-10-17-0801.43.pdiff [32.7 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources T-2021-10-18-0201.36-F-2021-10-17-0801.43.pdiff [32.7 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-10-18-0201.36-F-2021-10-17-0801.43.pdiff [44.8 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages T-2021-10-18-0201.36-F-2021-10-17-0801.43.pdiff [44.8 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main armhf Packages [8477 kB] Fetched 8846 kB in 4s (2406 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: tzdata 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 291 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 tzdata all 2021d-1 [291 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 291 kB in 0s (18.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 10545 files and directories currently installed.) Preparing to unpack .../tzdata_2021d-1_all.deb ... Unpacking tzdata (2021d-1) over (2021c-3) ... Setting up tzdata (2021d-1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Oct 18 04:57:34 UTC 2021. Universal Time is now: Mon Oct 18 04:57:34 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'berkeley-express' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/berkeley-express.git Please use: git clone https://salsa.debian.org/med-team/berkeley-express.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 379 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main berkeley-express 1.5.3+dfsg-2 (dsc) [2493 B] Get:2 http://debian.oregonstate.edu/debian unstable/main berkeley-express 1.5.3+dfsg-2 (tar) [366 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main berkeley-express 1.5.3+dfsg-2 (diff) [10.5 kB] Fetched 379 kB in 0s (23.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/berkeley-express-8Jviad/berkeley-express-1.5.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-8Jviad' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, libgoogle-perftools-dev, cmake, libprotobuf-dev, protobuf-compiler, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper-compat (= 13), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, libgoogle-perftools-dev, cmake, libprotobuf-dev, protobuf-compiler, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf 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 [512 B] Get:5 copy:/<>/apt_archive ./ Packages [567 B] Fetched 2036 B in 0s (83.4 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdextrautils build-essential cmake cmake-data cpp-11-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dpkg-cross dpkg-dev dwz emacsen-common file g++ g++-11 g++-11-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-10-base:armhf gcc-11-arm-linux-gnueabihf gcc-11-arm-linux-gnueabihf-base gcc-11-base:armhf gcc-11-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasan6:armhf libasan6-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbamtools-dev:armhf libbamtools2.5.1:armhf libboost-atomic1.74-dev:armhf libboost-atomic1.74.0:armhf libboost-chrono1.74-dev:armhf libboost-chrono1.74.0:armhf libboost-date-time-dev:armhf libboost-date-time1.74-dev:armhf libboost-date-time1.74.0:armhf libboost-filesystem-dev:armhf libboost-filesystem1.74-dev:armhf libboost-filesystem1.74.0:armhf libboost-program-options-dev:armhf libboost-program-options1.74-dev:armhf libboost-program-options1.74.0:armhf libboost-serialization1.74-dev:armhf libboost-serialization1.74.0:armhf libboost-system-dev:armhf libboost-system1.74-dev:armhf libboost-system1.74.0:armhf libboost-thread-dev:armhf libboost-thread1.74-dev:armhf libboost-thread1.74.0:armhf libboost-tools-dev libboost1.74-dev:armhf libboost1.74-tools-dev libbrotli1 libc6:armhf libc6-armhf-cross libc6-dev libc6-dev:armhf libc6-dev-armhf-cross libcom-err2:armhf libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:armhf libcrypt1:armhf libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:armhf libgcc-11-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libgomp1:armhf libgomp1-armhf-cross libgoogle-perftools-dev:armhf libgoogle-perftools4:armhf libgssapi-krb5-2:armhf libicu67 libio-string-perl libjsoncpp24 libk5crypto3:armhf libkeyutils1:armhf libkrb5-3:armhf libkrb5support0:armhf libldap-2.4-2 liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libnsl-dev libnsl-dev:armhf libnsl2:armhf libperl5.32 libpipeline1 libprocps8 libprotobuf-dev:armhf libprotobuf-lite23:armhf libprotobuf23 libprotobuf23:armhf libprotoc23 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1:armhf libstdc++-10-dev:armhf libstdc++-11-dev libstdc++-11-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtcmalloc-minimal4:armhf libtirpc-dev libtirpc-dev:armhf libtirpc3:armhf libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libuv1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db perl perl-modules-5.32 po-debconf procps protobuf-compiler rpcsvc-proto sensible-utils ucf zlib1g:armhf zlib1g-dev:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc ninja-build gcc-11-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-11-multilib gcc-11-doc manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc:armhf libboost1.74-doc:armhf libboost-container1.74-dev:armhf libboost-context1.74-dev:armhf libboost-contract1.74-dev:armhf libboost-coroutine1.74-dev:armhf libboost-exception1.74-dev:armhf libboost-fiber1.74-dev:armhf libboost-graph1.74-dev:armhf libboost-graph-parallel1.74-dev:armhf libboost-iostreams1.74-dev:armhf libboost-locale1.74-dev:armhf libboost-log1.74-dev:armhf libboost-math1.74-dev:armhf libboost-mpi1.74-dev:armhf libboost-mpi-python1.74-dev:armhf libboost-numpy1.74-dev:armhf libboost-python1.74-dev:armhf libboost-random1.74-dev:armhf libboost-regex1.74-dev:armhf libboost-stacktrace1.74-dev:armhf libboost-test1.74-dev:armhf libboost-timer1.74-dev:armhf libboost-type-erasure1.74-dev:armhf libboost-wave1.74-dev:armhf libmpfrc++-dev:armhf libntl-dev:armhf libboost-nowide1.74-dev:armhf xsltproc doxygen docbook-xml docbook-xsl default-jdk fop glibc-doc:armhf libc-l10n:armhf locales:armhf libnss-nis:armhf libnss-nisplus:armhf glibc-doc manpages-dev:armhf gnupg git bzr krb5-doc:armhf krb5-user:armhf libstdc++-10-doc:armhf libstdc++-11-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl protobuf-mode-el Recommended packages: gnupg libalgorithm-merge-perl curl | wget | lynx libidn2-0:armhf ca-certificates libfile-fcntllock-perl libarchive-cpio-perl krb5-locales:armhf libldap-common libgpm2 publicsuffix libsasl2-modules libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl psmisc libprotobuf-dev The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdextrautils build-essential cmake cmake-data cpp-11-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dpkg-cross dpkg-dev dwz emacsen-common file g++ g++-11 g++-11-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-10-base:armhf gcc-11-arm-linux-gnueabihf gcc-11-arm-linux-gnueabihf-base gcc-11-base:armhf gcc-11-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasan6:armhf libasan6-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbamtools-dev:armhf libbamtools2.5.1:armhf libboost-atomic1.74-dev:armhf libboost-atomic1.74.0:armhf libboost-chrono1.74-dev:armhf libboost-chrono1.74.0:armhf libboost-date-time-dev:armhf libboost-date-time1.74-dev:armhf libboost-date-time1.74.0:armhf libboost-filesystem-dev:armhf libboost-filesystem1.74-dev:armhf libboost-filesystem1.74.0:armhf libboost-program-options-dev:armhf libboost-program-options1.74-dev:armhf libboost-program-options1.74.0:armhf libboost-serialization1.74-dev:armhf libboost-serialization1.74.0:armhf libboost-system-dev:armhf libboost-system1.74-dev:armhf libboost-system1.74.0:armhf libboost-thread-dev:armhf libboost-thread1.74-dev:armhf libboost-thread1.74.0:armhf libboost-tools-dev libboost1.74-dev:armhf libboost1.74-tools-dev libbrotli1 libc6:armhf libc6-armhf-cross libc6-dev libc6-dev:armhf libc6-dev-armhf-cross libcom-err2:armhf libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev libcrypt-dev:armhf libcrypt1:armhf libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:armhf libgcc-11-dev-armhf-cross libgcc-s1:armhf libgcc-s1-armhf-cross libgomp1:armhf libgomp1-armhf-cross libgoogle-perftools-dev:armhf libgoogle-perftools4:armhf libgssapi-krb5-2:armhf libicu67 libio-string-perl libjsoncpp24 libk5crypto3:armhf libkeyutils1:armhf libkrb5-3:armhf libkrb5support0:armhf libldap-2.4-2 liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libnsl-dev libnsl-dev:armhf libnsl2:armhf libperl5.32 libpipeline1 libprocps8 libprotobuf-dev:armhf libprotobuf-lite23:armhf libprotobuf23 libprotobuf23:armhf libprotoc23 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1:armhf libstdc++-10-dev:armhf libstdc++-11-dev libstdc++-11-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtcmalloc-minimal4:armhf libtirpc-dev libtirpc-dev:armhf libtirpc3:armhf libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libuv1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db perl perl-modules-5.32 po-debconf procps protobuf-compiler rpcsvc-proto sbuild-build-depends-main-dummy:armhf sensible-utils ucf zlib1g:armhf zlib1g-dev:armhf 0 upgraded, 167 newly installed, 0 to remove and 0 not upgraded. Need to get 302 MB of archives. After this operation, 1203 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [992 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.37.2-3 [143 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-7 [935 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.32 all 5.32.1-6 [2824 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.32 amd64 5.32.1-6 [4106 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.32.1-6 [293 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main armhf gcc-10-base armhf 10.3.0-11 [206 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main armhf gcc-11-base armhf 11.2.0-9 [205 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.2+20210905-1 [102 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.39-3 [69.1 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.71-2 [343 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.4-2 [819 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.21-4 [510 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.37-7 [2865 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.25-2 [104 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 rpcsvc-proto amd64 1.4.2-4 [63.1 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.32-4 [2251 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-11-dev amd64 11.2.0-9 [1949 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 g++-11 amd64 11.2.0-9 [49.7 MB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:11.2.0-2 [1636 B] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.9 [1537 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.9 [2153 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.9 [7704 B] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.12+dfsg-5 [696 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.59+dfsg-1 [232 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libssh2-1 amd64 1.10.0-2 [178 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libcurl4 amd64 7.74.0-1.3+b1 [341 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.4.1-2+b1 [104 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libjsoncpp24 amd64 1.9.4-5 [78.8 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 librhash0 amd64 1.4.2-1 [129 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libuv1 amd64 1.42.0-1 [135 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 dh-elpa-helper all 2.0.9 [11.2 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 emacsen-common all 3.0.4 [19.3 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 cmake-data all 3.21.3-4 [1878 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 cmake amd64 3.21.3-4 [7887 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-arm-linux-gnueabihf-base amd64 11.2.0-9cross1 [205 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-11-arm-linux-gnueabihf amd64 11.2.0-9cross1 [48.3 MB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:11.2.0-2 [17.0 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-cross-base all 11.2.0-9cross1 [201 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.32-1cross4 [1100 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armhf-cross all 11.2.0-9cross1 [36.4 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 11.2.0-9cross1 [86.5 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 11.2.0-9cross1 [6676 B] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libasan6-armhf-cross all 11.2.0-9cross1 [1963 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 11.2.0-9cross1 [438 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 11.2.0-9cross1 [797 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-11-dev-armhf-cross all 11.2.0-9cross1 [711 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-11-arm-linux-gnueabihf amd64 11.2.0-9cross1 [54.8 MB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:11.2.0-2 [1460 B] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 5.10.46-4cross4 [1436 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.32-1cross4 [1762 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-11-dev-armhf-cross all 11.2.0-9cross1 [1960 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 g++-11-arm-linux-gnueabihf amd64 11.2.0-9cross1 [52.4 MB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:11.2.0-2 [1180 B] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2+b1 [337 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.9 [6708 B] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.5.2 [192 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-15 [513 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.185-2 [172 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.21-4 [1311 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.5.2 [1056 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-s1 armhf 11.2.0-9 [36.4 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.32-4 [2340 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armhf libasan6 armhf 11.2.0-9 [1971 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 11.2.0-9 [6908 B] Get:111 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 11.2.0-9 [479 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g armhf 1:1.2.11.dfsg-2 [85.4 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-9 [141 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main armhf libbamtools-dev armhf 2.5.1+dfsg-9 [195 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 11.2.0-9 [88.7 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 11.2.0-9 [798 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-10-dev armhf 10.3.0-11 [690 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 5.14.12-1 [1399 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main armhf libcrypt1 armhf 1:4.4.25-2 [96.8 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main armhf libcrypt-dev armhf 1:4.4.25-2 [112 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main armhf libcom-err2 armhf 1.46.4-1 [74.4 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main armhf libkrb5support0 armhf 1.18.3-7 [62.5 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main armhf libk5crypto3 armhf 1.18.3-7 [110 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main armhf libkeyutils1 armhf 1.6.1-2 [14.4 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main armhf libssl1.1 armhf 1.1.1l-1 [1311 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main armhf libkrb5-3 armhf 1.18.3-7 [319 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main armhf libgssapi-krb5-2 armhf 1.18.3-7 [143 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main armhf libtirpc3 armhf 1.3.2-2 [72.7 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main armhf libnsl2 armhf 1.3.0-2 [33.9 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main armhf libtirpc-dev armhf 1.3.2-2 [182 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main armhf libnsl-dev armhf 1.3.0-2 [62.1 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.32-4 [1793 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-10-dev armhf 10.3.0-11 [1810 kB] Get:134 http://debian.oregonstate.edu/debian unstable/main armhf libboost1.74-dev armhf 1.74.0-11 [9533 kB] Get:135 http://debian.oregonstate.edu/debian unstable/main armhf libboost-atomic1.74.0 armhf 1.74.0-11 [244 kB] Get:136 http://debian.oregonstate.edu/debian unstable/main armhf libboost-atomic1.74-dev armhf 1.74.0-11 [245 kB] Get:137 http://debian.oregonstate.edu/debian unstable/main armhf libboost-chrono1.74.0 armhf 1.74.0-11 [248 kB] Get:138 http://debian.oregonstate.edu/debian unstable/main armhf libboost-chrono1.74-dev armhf 1.74.0-11 [255 kB] Get:139 http://debian.oregonstate.edu/debian unstable/main armhf libboost-date-time1.74.0 armhf 1.74.0-11 [242 kB] Get:140 http://debian.oregonstate.edu/debian unstable/main armhf libboost-serialization1.74.0 armhf 1.74.0-11 [321 kB] Get:141 http://debian.oregonstate.edu/debian unstable/main armhf libboost-serialization1.74-dev armhf 1.74.0-11 [392 kB] Get:142 http://debian.oregonstate.edu/debian unstable/main armhf libboost-date-time1.74-dev armhf 1.74.0-11 [251 kB] Get:143 http://debian.oregonstate.edu/debian unstable/main armhf libboost-date-time-dev armhf 1.74.0.3 [4332 B] Get:144 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem1.74.0 armhf 1.74.0-11 [275 kB] Get:145 http://debian.oregonstate.edu/debian unstable/main armhf libboost-system1.74.0 armhf 1.74.0-11 [242 kB] Get:146 http://debian.oregonstate.edu/debian unstable/main armhf libboost-system1.74-dev armhf 1.74.0-11 [243 kB] Get:147 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem1.74-dev armhf 1.74.0-11 [289 kB] Get:148 http://debian.oregonstate.edu/debian unstable/main armhf libboost-filesystem-dev armhf 1.74.0.3 [4368 B] Get:149 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options1.74.0 armhf 1.74.0-11 [339 kB] Get:150 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options1.74-dev armhf 1.74.0-11 [383 kB] Get:151 http://debian.oregonstate.edu/debian unstable/main armhf libboost-program-options-dev armhf 1.74.0.3 [4340 B] Get:152 http://debian.oregonstate.edu/debian unstable/main armhf libboost-system-dev armhf 1.74.0.3 [4468 B] Get:153 http://debian.oregonstate.edu/debian unstable/main armhf libboost-thread1.74.0 armhf 1.74.0-11 [271 kB] Get:154 http://debian.oregonstate.edu/debian unstable/main armhf libboost-thread1.74-dev armhf 1.74.0-11 [286 kB] Get:155 http://debian.oregonstate.edu/debian unstable/main armhf libboost-thread-dev armhf 1.74.0.3 [4356 B] Get:156 http://debian.oregonstate.edu/debian unstable/main amd64 libboost1.74-tools-dev amd64 1.74.0-11 [1462 kB] Get:157 http://debian.oregonstate.edu/debian unstable/main amd64 libboost-tools-dev amd64 1.74.0.3 [4508 B] Get:158 http://debian.oregonstate.edu/debian unstable/main armhf libtcmalloc-minimal4 armhf 2.9.1-1 [80.8 kB] Get:159 http://debian.oregonstate.edu/debian unstable/main armhf libgoogle-perftools4 armhf 2.9.1-1 [172 kB] Get:160 http://debian.oregonstate.edu/debian unstable/main armhf libgoogle-perftools-dev armhf 2.9.1-1 [450 kB] Get:161 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Get:162 http://debian.oregonstate.edu/debian unstable/main armhf libprotobuf23 armhf 3.12.4-1 [777 kB] Get:163 http://debian.oregonstate.edu/debian unstable/main armhf libprotobuf-lite23 armhf 3.12.4-1 [217 kB] Get:164 http://debian.oregonstate.edu/debian unstable/main armhf libprotobuf-dev armhf 3.12.4-1 [1192 kB] Get:165 http://debian.oregonstate.edu/debian unstable/main amd64 libprotobuf23 amd64 3.12.4-1 [892 kB] Get:166 http://debian.oregonstate.edu/debian unstable/main amd64 libprotoc23 amd64 3.12.4-1 [803 kB] Get:167 http://debian.oregonstate.edu/debian unstable/main amd64 protobuf-compiler amd64 3.12.4-1 [75.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 302 MB in 2s (130 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10545 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.37.2-3_amd64.deb ... Unpacking bsdextrautils (2.37.2-3) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../001-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-7_amd64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../003-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package perl-modules-5.32. Preparing to unpack .../005-perl-modules-5.32_5.32.1-6_all.deb ... Unpacking perl-modules-5.32 (5.32.1-6) ... Selecting previously unselected package libperl5.32:amd64. Preparing to unpack .../006-libperl5.32_5.32.1-6_amd64.deb ... Unpacking libperl5.32:amd64 (5.32.1-6) ... Selecting previously unselected package perl. Preparing to unpack .../007-perl_5.32.1-6_amd64.deb ... Unpacking perl (5.32.1-6) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../008-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package gcc-10-base:armhf. Preparing to unpack .../009-gcc-10-base_10.3.0-11_armhf.deb ... Unpacking gcc-10-base:armhf (10.3.0-11) ... Selecting previously unselected package gcc-11-base:armhf. Preparing to unpack .../010-gcc-11-base_11.2.0-9_armhf.deb ... Unpacking gcc-11-base:armhf (11.2.0-9) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../011-libncurses6_6.2+20210905-1_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20210905-1) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../012-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../013-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../014-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../015-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../016-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../017-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../018-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../019-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../020-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../021-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../022-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../023-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../024-automake_1%3a1.16.4-2_all.deb ... Unpacking automake (1:1.16.4-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../025-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package binutils-arm-linux-gnueabihf. Preparing to unpack .../026-binutils-arm-linux-gnueabihf_2.37-7_amd64.deb ... Unpacking binutils-arm-linux-gnueabihf (2.37-7) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../027-libcrypt-dev_1%3a4.4.25-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.25-2) ... Selecting previously unselected package libtirpc-dev:amd64. Preparing to unpack .../028-libtirpc-dev_1.3.2-2_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.2-2) ... Selecting previously unselected package libnsl-dev:amd64. Preparing to unpack .../029-libnsl-dev_1.3.0-2_amd64.deb ... Unpacking libnsl-dev:amd64 (1.3.0-2) ... Selecting previously unselected package rpcsvc-proto. Preparing to unpack .../030-rpcsvc-proto_1.4.2-4_amd64.deb ... Unpacking rpcsvc-proto (1.4.2-4) ... Selecting previously unselected package libc6-dev:amd64. Preparing to unpack .../031-libc6-dev_2.32-4_amd64.deb ... Unpacking libc6-dev:amd64 (2.32-4) ... Selecting previously unselected package libstdc++-11-dev:amd64. Preparing to unpack .../032-libstdc++-11-dev_11.2.0-9_amd64.deb ... Unpacking libstdc++-11-dev:amd64 (11.2.0-9) ... Selecting previously unselected package g++-11. Preparing to unpack .../033-g++-11_11.2.0-9_amd64.deb ... Unpacking g++-11 (11.2.0-9) ... Selecting previously unselected package g++. Preparing to unpack .../034-g++_4%3a11.2.0-2_amd64.deb ... Unpacking g++ (4:11.2.0-2) ... Selecting previously unselected package libdpkg-perl. Preparing to unpack .../035-libdpkg-perl_1.20.9_all.deb ... Unpacking libdpkg-perl (1.20.9) ... Selecting previously unselected package dpkg-dev. Preparing to unpack .../036-dpkg-dev_1.20.9_all.deb ... Unpacking dpkg-dev (1.20.9) ... Selecting previously unselected package build-essential. Preparing to unpack .../037-build-essential_12.9_amd64.deb ... Unpacking build-essential (12.9) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../038-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../039-libxml2_2.9.12+dfsg-5_amd64.deb ... Unpacking libxml2:amd64 (2.9.12+dfsg-5) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../040-libarchive13_3.4.3-2+b1_amd64.deb ... Unpacking libarchive13:amd64 (3.4.3-2+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../041-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../042-libsasl2-modules-db_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... 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Setting up libconfig-inifiles-perl (3.000003-1) ... Setting up libexpat1:amd64 (2.4.1-2+b1) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libboost-system1.74.0:armhf (1.74.0-11) ... Setting up gcc-11-base:armhf (11.2.0-9) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up libc6-armhf-cross (2.32-1cross4) ... Setting up bsdextrautils (2.37.2-3) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up perl-modules-5.32 (5.32.1-6) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up linux-libc-dev:armhf (5.14.12-1) ... Setting up gettext-base (0.21-4) ... Setting up libprotobuf23:amd64 (3.12.4-1) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up gcc-10-base:armhf (10.3.0-11) ... 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Processing triggers for libc-bin (2.32-4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) amd64 (x86_64) Toolchain package versions: binutils_2.37-7 dpkg-dev_1.20.9 g++-11_11.2.0-9 gcc-11_11.2.0-9 libc6-dev_2.32-4 libstdc++-10-dev_10.3.0-11 libstdc++-11-dev_11.2.0-9 libstdc++-11-dev-armhf-cross_11.2.0-9cross1 libstdc++6_11.2.0-9 libstdc++6-armhf-cross_11.2.0-9cross1 linux-libc-dev_5.14.12-1 Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 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Binary: berkeley-express, berkeley-express-doc Architecture: any all Version: 1.5.3+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: http://bio.math.berkeley.edu/eXpress/index.html Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/berkeley-express Vcs-Git: https://salsa.debian.org/med-team/berkeley-express.git Testsuite: autopkgtest Testsuite-Triggers: bowtie, gzip, samtools Build-Depends: debhelper-compat (= 13), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, libgoogle-perftools-dev [amd64 arm64 armel armhf i386 powerpc ppc64el], cmake, libprotobuf-dev, protobuf-compiler Package-List: berkeley-express deb science optional arch=any berkeley-express-doc deb doc optional arch=all Checksums-Sha1: a24eee0a32da390f2f75be7526bf6a9a971bd3a3 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz 2213d960a0ef02dd989468cc4e3b90d599c47581 10544 berkeley-express_1.5.3+dfsg-2.debian.tar.xz Checksums-Sha256: f26e2f6e4e04671a64619f014ab2195f42d53fbac8b8b84f46082c5cdc6d845b 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz c66387e6e0cc20b77b55570759b37f8e4bded1fdcab94ca229226bcbdf998bb1 10544 berkeley-express_1.5.3+dfsg-2.debian.tar.xz Files: cdb0c73b54ec20a662c14e6bfee0e384 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz aaa3d9f3529081d0d75de24ef205c9e6 10544 berkeley-express_1.5.3+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFm0eURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH3Og//YgO0vDL4EQDtN4ReFUAPcCzQlkpXna0R LLfAM56Bltoxn1DJ9Rb8Xhfyzp/llkbXTDn4ITz6VCd66UNCR7Nb7nkQVvFdkf1y k3uTx/u6oh5mFbCQ3l36A/amqhfzTnBU/eUSBcSl04hfMkh5nfq7lD4ihWU59nqs fDaXSlbQK8aXs2f7qFHmR+iERPXOtTtjvWIh6s6wvpfnIrVgytw+S5uDAJHtZiFy Fw3o9FNlL5ToMkgQCmRFUhqE/Tpx7t92HMlKDfSXxCzq21Y++Y0jjnuZ7a//4qqv 87rfVLYyyvz/rTMPEXFkFeyVaNimBnjTOoYf51Em/hTPBKHsxZ/npiDd1f3OHYfJ yg3OH3XBQ8uplx3PMx0CtTkN6lGHtTHRyvnEyAtZby6pz944VK6sj2o63oanNvjj a9Ll9mseGM2CfjhwUw0NhBoeZSF/NSzYNDMDhDTKuahcOvLV8WxkgJGD4UrJAIUY 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fix-bamtools-path dpkg-source: info: applying drop-zlib dpkg-source: info: applying correct-debug-flags.patch dpkg-source: info: applying privacy-breach.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.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-fae70d87-c886-4bff-b711-4fdcb773dcb8 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package berkeley-express dpkg-buildpackage: info: source version 1.5.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf 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 armhf debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean src/config.h make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-arm-linux-gnueabihf && 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 -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=armv7l -DCMAKE_C_COMPILER=arm-linux-gnueabihf-gcc -DCMAKE_CXX_COMPILER=arm-linux-gnueabihf-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-qmake -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf .. CMake Deprecation Warning at CMakeLists.txt:1 (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 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/arm-linux-gnueabihf-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-gnueabihf-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/arm-linux-gnueabihf/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.39") found components: thread system filesystem program_options date_time -- Found GPERFTOOLS_TCMALLOC: /usr/lib/arm-linux-gnueabihf/libtcmalloc.so -- Found Protobuf: /usr/lib/arm-linux-gnueabihf/libprotobuf.so;-lpthread (found version "3.12.4") -- Do not try to find libbamtools.a -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE QMAKE_EXECUTABLE -- Build files have been written to: /<>/obj-arm-linux-gnueabihf dh_auto_build -a cd obj-arm-linux-gnueabihf && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles /<>/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 5%] Running cpp protocol buffer compiler on /<>/src/targets.proto cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/protoc --cpp_out /<>/obj-arm-linux-gnueabihf/src -I /<>/src /<>/src/targets.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:648] No syntax specified for the proto file: targets.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [ 11%] Running cpp protocol buffer compiler on /<>/src/alignments.proto cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/protoc --cpp_out /<>/obj-arm-linux-gnueabihf/src -I /<>/src /<>/src/alignments.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:648] No syntax specified for the proto file: alignments.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src /<>/obj-arm-linux-gnueabihf/src/CMakeFiles/express.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 16%] Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/biascorrection.cpp.o -MF CMakeFiles/express.dir/biascorrection.cpp.o.d -o CMakeFiles/express.dir/biascorrection.cpp.o -c /<>/src/biascorrection.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 22%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/bundles.cpp.o -MF CMakeFiles/express.dir/bundles.cpp.o.d -o CMakeFiles/express.dir/bundles.cpp.o -c /<>/src/bundles.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 27%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/directiondetector.cpp.o -MF CMakeFiles/express.dir/directiondetector.cpp.o.d -o CMakeFiles/express.dir/directiondetector.cpp.o -c /<>/src/directiondetector.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 33%] Building CXX object src/CMakeFiles/express.dir/fragments.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/fragments.cpp.o -MF CMakeFiles/express.dir/fragments.cpp.o.d -o CMakeFiles/express.dir/fragments.cpp.o -c /<>/src/fragments.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 38%] Building CXX object src/CMakeFiles/express.dir/lengthdistribution.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/lengthdistribution.cpp.o -MF CMakeFiles/express.dir/lengthdistribution.cpp.o.d -o CMakeFiles/express.dir/lengthdistribution.cpp.o -c /<>/src/lengthdistribution.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] In file included from /usr/arm-linux-gnueabihf/include/c++/11/vector:72, from /<>/src/lengthdistribution.h:12, from /<>/src/lengthdistribution.cpp:9: /usr/arm-linux-gnueabihf/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabihf/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/11/bits/vector.tcc: In constructor ‘LengthDistribution::LengthDistribution(std::string, std::string)’: /usr/arm-linux-gnueabihf/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object src/CMakeFiles/express.dir/main.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/main.cpp.o -MF CMakeFiles/express.dir/main.cpp.o.d -o CMakeFiles/express.dir/main.cpp.o -c /<>/src/main.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 50%] Building CXX object src/CMakeFiles/express.dir/mapparser.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/mapparser.cpp.o -MF CMakeFiles/express.dir/mapparser.cpp.o.d -o CMakeFiles/express.dir/mapparser.cpp.o -c /<>/src/mapparser.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 55%] Building CXX object src/CMakeFiles/express.dir/markovmodel.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/markovmodel.cpp.o -MF CMakeFiles/express.dir/markovmodel.cpp.o.d -o CMakeFiles/express.dir/markovmodel.cpp.o -c /<>/src/markovmodel.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 61%] Building CXX object src/CMakeFiles/express.dir/mismatchmodel.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/mismatchmodel.cpp.o -MF CMakeFiles/express.dir/mismatchmodel.cpp.o.d -o CMakeFiles/express.dir/mismatchmodel.cpp.o -c /<>/src/mismatchmodel.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 66%] Building CXX object src/CMakeFiles/express.dir/robertsfilter.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/robertsfilter.cpp.o -MF CMakeFiles/express.dir/robertsfilter.cpp.o.d -o CMakeFiles/express.dir/robertsfilter.cpp.o -c /<>/src/robertsfilter.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 72%] Building CXX object src/CMakeFiles/express.dir/sequence.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/sequence.cpp.o -MF CMakeFiles/express.dir/sequence.cpp.o.d -o CMakeFiles/express.dir/sequence.cpp.o -c /<>/src/sequence.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 77%] Building CXX object src/CMakeFiles/express.dir/targets.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/targets.cpp.o -MF CMakeFiles/express.dir/targets.cpp.o.d -o CMakeFiles/express.dir/targets.cpp.o -c /<>/src/targets.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 83%] Building CXX object src/CMakeFiles/express.dir/threadsafety.cpp.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/threadsafety.cpp.o -MF CMakeFiles/express.dir/threadsafety.cpp.o.d -o CMakeFiles/express.dir/threadsafety.cpp.o -c /<>/src/threadsafety.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 88%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/alignments.pb.cc.o -MF CMakeFiles/express.dir/alignments.pb.cc.o.d -o CMakeFiles/express.dir/alignments.pb.cc.o -c /<>/obj-arm-linux-gnueabihf/src/alignments.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 94%] Building CXX object src/CMakeFiles/express.dir/targets.pb.cc.o cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/arm-linux-gnueabihf-g++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/targets.pb.cc.o -MF CMakeFiles/express.dir/targets.pb.cc.o.d -o CMakeFiles/express.dir/targets.pb.cc.o -c /<>/obj-arm-linux-gnueabihf/src/targets.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [100%] Linking CXX executable express cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/express.dir/link.txt --verbose=1 /usr/bin/arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/express.dir/biascorrection.cpp.o CMakeFiles/express.dir/bundles.cpp.o CMakeFiles/express.dir/directiondetector.cpp.o CMakeFiles/express.dir/fragments.cpp.o CMakeFiles/express.dir/lengthdistribution.cpp.o CMakeFiles/express.dir/main.cpp.o CMakeFiles/express.dir/mapparser.cpp.o CMakeFiles/express.dir/markovmodel.cpp.o CMakeFiles/express.dir/mismatchmodel.cpp.o CMakeFiles/express.dir/robertsfilter.cpp.o CMakeFiles/express.dir/sequence.cpp.o CMakeFiles/express.dir/targets.cpp.o CMakeFiles/express.dir/threadsafety.cpp.o CMakeFiles/express.dir/alignments.pb.cc.o CMakeFiles/express.dir/targets.pb.cc.o -o express /usr/lib/arm-linux-gnueabihf/libboost_thread.so.1.74.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.74.0 /usr/lib/arm-linux-gnueabihf/libboost_filesystem.so.1.74.0 /usr/lib/arm-linux-gnueabihf/libboost_program_options.so.1.74.0 /usr/lib/arm-linux-gnueabihf/libboost_date_time.so.1.74.0 -lbamtools -lprotobuf -lpthread -lrt /usr/lib/arm-linux-gnueabihf/libboost_atomic.so.1.74.0 -lpthread make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target express make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' 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_installdirs -a dh_auto_install -a cd obj-arm-linux-gnueabihf && make -j1 install DESTDIR=/<>/berkeley-express-1.5.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/bin/express make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=express-doc.pdf make[1]: Leaving directory '/<>' dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/berkeley-express/usr/lib/debian-med/bin/express contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'berkeley-express' in '../berkeley-express_1.5.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'berkeley-express-dbgsym' in '../berkeley-express-dbgsym_1.5.3+dfsg-2_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../berkeley-express_1.5.3+dfsg-2_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-10-18T05:00:22Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ berkeley-express_1.5.3+dfsg-2_armhf.changes: -------------------------------------------- Format: 1.8 Date: Wed, 13 Oct 2021 14:29:57 +0200 Source: berkeley-express Binary: berkeley-express berkeley-express-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 1.5.3+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: berkeley-express - Streaming quantification for high-throughput sequencing Changes: berkeley-express (1.5.3+dfsg-2) unstable; urgency=medium . * Team upload. * Fix watchfile to detect new versions on github * Standards-Version: 4.6.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * No tab in license text (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. 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18 Oct 2021 05:00:21 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.4-2), autopoint (= 0.21-4), autotools-dev (= 20180224.1+nmu1), base-files (= 12), base-passwd (= 3.5.52), bash (= 5.1-3+b2), binutils (= 2.37-7), binutils-common (= 2.37-7), binutils-x86-64-linux-gnu (= 2.37-7), bsdextrautils (= 2.37.2-3), bsdutils (= 1:2.37.2-3), build-essential (= 12.9), bzip2 (= 1.0.8-4), cmake (= 3.21.3-4), cmake-data (= 3.21.3-4), coreutils (= 8.32-4+b1), cpp (= 4:11.2.0-2), cpp-11 (= 11.2.0-9), dash (= 0.5.11+git20210120+802ebd4-1), debconf (= 1.5.77), debhelper (= 13.5.2), debianutils (= 5.5-1), dh-autoreconf (= 20), dh-elpa-helper (= 2.0.9), dh-strip-nondeterminism (= 1.12.0-1), diffutils (= 1:3.7-5), dpkg (= 1.20.9), dpkg-dev (= 1.20.9), dwz (= 0.14-1), emacsen-common (= 3.0.4), file (= 1:5.39-3), findutils (= 4.8.0-1), g++ (= 4:11.2.0-2), g++-11 (= 11.2.0-9), gcc (= 4:11.2.0-2), gcc-10-base (= 10.3.0-11), gcc-11 (= 11.2.0-9), gcc-11-base (= 11.2.0-9), 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1.74.0-11), libboost-program-options1.74.0 (= 1.74.0-11), libboost-serialization1.74-dev (= 1.74.0-11), libboost-serialization1.74.0 (= 1.74.0-11), libboost-system-dev (= 1.74.0.3), libboost-system1.74-dev (= 1.74.0-11), libboost-system1.74.0 (= 1.74.0-11), libboost-thread-dev (= 1.74.0.3), libboost-thread1.74-dev (= 1.74.0-11), libboost-thread1.74.0 (= 1.74.0-11), libboost-tools-dev (= 1.74.0.3), libboost1.74-dev (= 1.74.0-11), libboost1.74-tools-dev (= 1.74.0-11), libbrotli1 (= 1.0.9-2+b2), libbz2-1.0 (= 1.0.8-4), libc-bin (= 2.32-4), libc-dev-bin (= 2.32-4), libc6 (= 2.32-4), libc6-dev (= 2.32-4), libcap-ng0 (= 0.7.9-2.2+b1), libcap2 (= 1:2.44-1), libcc1-0 (= 11.2.0-9), libcom-err2 (= 1.46.4-1), libcrypt-dev (= 1:4.4.25-2), libcrypt1 (= 1:4.4.25-2), libctf-nobfd0 (= 2.37-7), libctf0 (= 2.37-7), libcurl4 (= 7.74.0-1.3+b1), libdb5.3 (= 5.3.28+dfsg1-0.8), libdebconfclient0 (= 0.260), libdebhelper-perl (= 13.5.2), libdpkg-perl (= 1.20.9), libelf1 (= 0.185-2), libexpat1 (= 2.4.1-2+b1), libffi8 (= 3.4.2-3), libfile-stripnondeterminism-perl (= 1.12.0-1), libgcc-10-dev (= 10.3.0-11), libgcc-11-dev (= 11.2.0-9), libgcc-s1 (= 11.2.0-9), libgcrypt20 (= 1.9.4-3+b1), libgdbm-compat4 (= 1.21-1), libgdbm6 (= 1.21-1), libgmp10 (= 2:6.2.1+dfsg-2), libgnutls30 (= 3.7.2-2), libgomp1 (= 11.2.0-9), libgoogle-perftools-dev (= 2.9.1-1), libgoogle-perftools4 (= 2.9.1-1), libgpg-error0 (= 1.42-3), libgssapi-krb5-2 (= 1.18.3-7), libhogweed6 (= 3.7.3-1), libicu67 (= 67.1-7), libidn2-0 (= 2.3.2-2), libisl23 (= 0.24-2), libitm1 (= 11.2.0-9), libjsoncpp24 (= 1.9.4-5), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), libldap-2.4-2 (= 2.4.59+dfsg-1), liblsan0 (= 11.2.0-9), liblz4-1 (= 1.9.3-2), liblzma5 (= 5.2.5-2), libmagic-mgc (= 1:5.39-3), libmagic1 (= 1:5.39-3), libmount1 (= 2.37.2-3), libmpc3 (= 1.2.1-1), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.2+20210905-1), libncursesw6 (= 6.2+20210905-1), libnettle8 (= 3.7.3-1), libnghttp2-14 (= 1.43.0-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libp11-kit0 (= 0.24.0-5), libpam-modules (= 1.4.0-10), libpam-modules-bin (= 1.4.0-10), libpam-runtime (= 1.4.0-10), libpam0g (= 1.4.0-10), libpcre2-8-0 (= 10.36-2), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.1-6), libpipeline1 (= 1.5.3-1), libprocps8 (= 2:3.3.17-5), libprotobuf-dev (= 3.12.4-1), libprotobuf-lite23 (= 3.12.4-1), libprotobuf23 (= 3.12.4-1), libprotoc23 (= 3.12.4-1), libpsl5 (= 0.21.0-1.2), libquadmath0 (= 11.2.0-9), librhash0 (= 1.4.2-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.27+dfsg-2.1), libsasl2-modules-db (= 2.1.27+dfsg-2.1), libseccomp2 (= 2.5.2-2), libselinux1 (= 3.1-3), libsigsegv2 (= 2.13-1), libsmartcols1 (= 2.37.2-3), libssh2-1 (= 1.10.0-2), libssl1.1 (= 1.1.1l-1), libstdc++-10-dev (= 10.3.0-11), libstdc++-11-dev (= 11.2.0-9), libstdc++6 (= 11.2.0-9), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.5-1), libtasn1-6 (= 4.17.0-2), libtcmalloc-minimal4 (= 2.9.1-1), libtinfo6 (= 6.2+20210905-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15), libtsan0 (= 11.2.0-9), libubsan1 (= 11.2.0-9), libuchardet0 (= 0.0.7-1), libudev1 (= 249.5-1), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-3), libuv1 (= 1.42.0-1), libxml2 (= 2.9.12+dfsg-5), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.14.12-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-5), make (= 4.3-4.1), man-db (= 2.9.4-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2+20210905-1), ncurses-bin (= 6.2+20210905-1), patch (= 2.7.6-7), perl (= 5.32.1-6), perl-base (= 5.32.1-6), perl-modules-5.32 (= 5.32.1-6), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-5), protobuf-compiler (= 3.12.4-1), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.00-1), tar (= 1.34+dfsg-1), util-linux (= 2.37.2-3), xz-utils (= 5.2.5-2), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1634128197" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ berkeley-express-dbgsym_1.5.3+dfsg-2_armhf.deb ---------------------------------------------- new Debian package, version 2.0. size 4273428 bytes: control archive=548 bytes. 417 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: berkeley-express-dbgsym Source: berkeley-express Version: 1.5.3+dfsg-2 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 4350 Depends: berkeley-express (= 1.5.3+dfsg-2) Section: debug Priority: optional Description: debug symbols for berkeley-express Build-Ids: 23f3001841b02e0c002831792e48ba13ab3f057e drwxr-xr-x root/root 0 2021-10-13 12:29 ./ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/lib/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/lib/debug/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/lib/debug/.build-id/23/ -rw-r--r-- root/root 4443872 2021-10-13 12:29 ./usr/lib/debug/.build-id/23/f3001841b02e0c002831792e48ba13ab3f057e.debug drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/share/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/share/doc/ lrwxrwxrwx root/root 0 2021-10-13 12:29 ./usr/share/doc/berkeley-express-dbgsym -> berkeley-express berkeley-express_1.5.3+dfsg-2_armhf.deb --------------------------------------- new Debian package, version 2.0. size 185792 bytes: control archive=1912 bytes. 3100 bytes, 50 lines control 454 bytes, 6 lines md5sums Package: berkeley-express Version: 1.5.3+dfsg-2 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 493 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libboost-filesystem1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libboost-thread1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.5), libprotobuf23 (>= 3.12.4), libstdc++6 (>= 11) Recommends: med-config Section: science Priority: optional Homepage: http://bio.math.berkeley.edu/eXpress/index.html Description: Streaming quantification for high-throughput sequencing eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk. . In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias. . eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance. drwxr-xr-x root/root 0 2021-10-13 12:29 ./ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/bin/ lrwxrwxrwx root/root 0 2021-10-13 12:29 ./usr/bin/berkeley-express -> ../lib/debian-med/bin/express drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/lib/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 481140 2021-10-13 12:29 ./usr/lib/debian-med/bin/express drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/share/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/share/doc/berkeley-express/ -rw-r--r-- root/root 987 2021-10-13 12:29 ./usr/share/doc/berkeley-express/README.Debian -rw-r--r-- root/root 1540 2019-11-14 16:14 ./usr/share/doc/berkeley-express/README.gz -rw-r--r-- root/root 1249 2021-10-13 12:29 ./usr/share/doc/berkeley-express/changelog.Debian.gz -rw-r--r-- root/root 2869 2021-10-13 12:29 ./usr/share/doc/berkeley-express/copyright drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/share/man/ drwxr-xr-x root/root 0 2021-10-13 12:29 ./usr/share/man/man1/ -rw-r--r-- root/root 1192 2021-10-13 12:29 ./usr/share/man/man1/berkeley-express.1.gz 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 [646 B] Get:5 copy:/<>/apt_archive ./ Packages [702 B] Fetched 2311 B in 0s (85.9 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-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 libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils t1utils unzip Suggested packages: libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libwww-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg liblist-someutils-xs-perl libpackage-stash-xs-perl libref-util-perl libtype-tiny-xs-perl The following NEW packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-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 libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils sbuild-build-depends-lintian-dummy:armhf t1utils unzip 0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 7599 kB of archives. After this operation, 21.8 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.64-1 [36.6 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.5-1 [51.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.27-2 [547 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.36.0-2 [815 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.27-2 [927 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 libaliased-perl all 0.34-1.1 [14.1 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.40 [72.2 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b3 [11.3 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b2 [15.9 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b3 [25.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b3 [45.7 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.25-1 [19.5 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 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Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-messagepack-perl amd64 1.01-2 [35.5 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-size-perl amd64 0.83-1+b2 [26.1 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-address-xs-perl amd64 1.04-1+b3 [28.0 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.11-1 [8888 B] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libio-prompt-tiny-perl all 0.003-1 [9150 B] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.005004-2 [60.4 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libmouse-perl amd64 2.5.10-1+b1 [172 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b3 [12.0 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1+b1 [13.8 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.118-1 [53.5 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-gzip-perl amd64 0.19-1+b7 [17.4 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.008-1+b1 [12.0 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libproc-processtable-perl amd64 0.634-1 [46.5 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.018+ds-1+b1 [99.3 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.018+ds-1+b1 [103 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libsort-versions-perl all 1.62-1 [11.0 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-1+b2 [27.8 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-4+b8 [8724 B] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.13-1 [13.2 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.8-1+b1 [197 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-moment-perl amd64 0.44-1+b3 [75.8 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.012004-1 [351 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b2 [20.3 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 5.08-1 [90.6 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.83+ds-1 [35.5 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 lzip amd64 1.22-4 [88.2 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 unzip amd64 6.0-26 [171 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.109.0 [1338 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7599 kB in 0s (27.0 MB/s) Selecting previously unselected package diffstat. (Reading database ... 40605 files and directories currently installed.) Preparing to unpack .../00-diffstat_1.64-1_amd64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../01-libassuan0_2.5.5-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.5-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../02-gpgconf_2.2.27-2_amd64.deb ... Unpacking gpgconf (2.2.27-2) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../03-libsqlite3-0_3.36.0-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.36.0-2) ... Selecting previously unselected package gpg. Preparing to unpack .../04-gpg_2.2.27-2_amd64.deb ... Unpacking gpg (2.2.27-2) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../05-libaliased-perl_0.34-1.1_all.deb ... Unpacking libaliased-perl (0.34-1.1) ... Selecting previously unselected package libapt-pkg-perl. 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Selecting previously unselected package libpackage-stash-perl. Preparing to unpack .../65-libpackage-stash-perl_0.39-1_all.deb ... Unpacking libpackage-stash-perl (0.39-1) ... Selecting previously unselected package libsub-identify-perl. Preparing to unpack .../66-libsub-identify-perl_0.14-1+b3_amd64.deb ... Unpacking libsub-identify-perl (0.14-1+b3) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../67-libsub-name-perl_0.26-1+b1_amd64.deb ... Unpacking libsub-name-perl (0.26-1+b1) ... Selecting previously unselected package libnamespace-clean-perl. Preparing to unpack .../68-libnamespace-clean-perl_0.27-1_all.deb ... Unpacking libnamespace-clean-perl (0.27-1) ... Selecting previously unselected package libpath-tiny-perl. Preparing to unpack .../69-libpath-tiny-perl_0.118-1_all.deb ... Unpacking libpath-tiny-perl (0.118-1) ... Selecting previously unselected package libperlio-gzip-perl. Preparing to unpack .../70-libperlio-gzip-perl_0.19-1+b7_amd64.deb ... Unpacking libperlio-gzip-perl (0.19-1+b7) ... Selecting previously unselected package libperlio-utf8-strict-perl. Preparing to unpack .../71-libperlio-utf8-strict-perl_0.008-1+b1_amd64.deb ... Unpacking libperlio-utf8-strict-perl (0.008-1+b1) ... Selecting previously unselected package libproc-processtable-perl:amd64. Preparing to unpack .../72-libproc-processtable-perl_0.634-1_amd64.deb ... Unpacking libproc-processtable-perl:amd64 (0.634-1) ... Selecting previously unselected package libsereal-decoder-perl. Preparing to unpack .../73-libsereal-decoder-perl_4.018+ds-1+b1_amd64.deb ... Unpacking libsereal-decoder-perl (4.018+ds-1+b1) ... Selecting previously unselected package libsereal-encoder-perl. Preparing to unpack .../74-libsereal-encoder-perl_4.018+ds-1+b1_amd64.deb ... Unpacking libsereal-encoder-perl (4.018+ds-1+b1) ... Selecting previously unselected package libsort-versions-perl. Preparing to unpack .../75-libsort-versions-perl_1.62-1_all.deb ... Unpacking libsort-versions-perl (1.62-1) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../76-libterm-readkey-perl_2.38-1+b2_amd64.deb ... Unpacking libterm-readkey-perl (2.38-1+b2) ... Selecting previously unselected package libtext-levenshteinxs-perl. Preparing to unpack .../77-libtext-levenshteinxs-perl_0.03-4+b8_amd64.deb ... Unpacking libtext-levenshteinxs-perl (0.03-4+b8) ... Selecting previously unselected package libtext-markdown-discount-perl:amd64. Preparing to unpack .../78-libtext-markdown-discount-perl_0.13-1_amd64.deb ... Unpacking libtext-markdown-discount-perl:amd64 (0.13-1) ... Selecting previously unselected package libtext-xslate-perl. Preparing to unpack .../79-libtext-xslate-perl_3.5.8-1+b1_amd64.deb ... Unpacking libtext-xslate-perl (3.5.8-1+b1) ... Selecting previously unselected package libtime-duration-perl. 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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: 67464 Build-Time: 119 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 48 Job: berkeley-express_1.5.3+dfsg-2 Lintian: pass Machine Architecture: amd64 Package: berkeley-express Package-Time: 182 Source-Version: 1.5.3+dfsg-2 Space: 67464 Status: successful Version: 1.5.3+dfsg-2 -------------------------------------------------------------------------------- Finished at 2021-10-18T05:00:22Z Build needed 00:03:02, 67464k disk space