https://launchpad.net/ubuntu/+source/augustus/3.3.3+dfsg-2build1/+build/19100189 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-047 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 6 Apr 12:02:03 ntpdate[279678]: adjust time server 10.211.37.1 offset -0.000006 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100189 --image-type chroot /home/buildd/filecache-default/88ad86cb2b525f1abddded96eadf8014548f7845 Creating target for build PACKAGEBUILD-19100189 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100189 Starting target for build PACKAGEBUILD-19100189 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100189 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-19100189 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100189 Updating target for build PACKAGEBUILD-19100189 Ign:1 http://archive-team.internal/bootstrap/riscv64 focal InRelease Get:2 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal Release [757 B] Ign:4 http://archive-team.internal/bootstrap/riscv64 focal Release.gpg Get:5 http://ftpmaster.internal/ubuntu focal-proposed InRelease [265 kB] Get:6 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 Packages [200 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 Packages [817 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main Translation-en [501 kB] Get:9 http://ftpmaster.internal/ubuntu focal/universe riscv64 Packages [6704 kB] Get:10 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5128 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 Packages [45.4 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [36.1 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/restricted Translation-en [860 B] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 Packages [121 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [112 kB] Get:16 http://ftpmaster.internal/ubuntu focal-proposed/multiverse riscv64 Packages [1140 B] Fetched 14.2 MB in 27s (521 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt coreutils cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base libapt-pkg6.0 libc-bin libc-dev-bin libc6 libc6-dev libgcc-9-dev libgnutls30 liblocale-gettext-perl libperl5.30 libstdc++-9-dev libsystemd0 libtext-charwidth-perl libtext-iconv-perl libudev1 perl-base 22 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 39.4 MB of archives. After this operation, 329 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu focal/main riscv64 coreutils riscv64 8.30-3ubuntu2 [1158 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 perl-base riscv64 5.30.0-9build1 [1419 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 libc6-dev riscv64 2.31-0ubuntu7 [3659 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libc-dev-bin riscv64 2.31-0ubuntu7 [62.5 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libc6 riscv64 2.31-0ubuntu7 [2272 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libc-bin riscv64 2.31-0ubuntu7 [505 kB] Get:7 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libsystemd0 riscv64 245.2-1ubuntu3 [242 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libudev1 riscv64 245.2-1ubuntu3 [69.0 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libapt-pkg6.0 riscv64 2.0.1ubuntu1 [797 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libgnutls30 riscv64 3.6.13-2ubuntu1 [720 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 apt riscv64 2.0.1ubuntu1 [1231 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 liblocale-gettext-perl riscv64 1.07-4 [16.5 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-charwidth-perl riscv64 0.04-10 [9460 B] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-iconv-perl riscv64 1.7-7 [13.2 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 g++-9 riscv64 9.3.0-10ubuntu1 [6926 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 gcc-9 riscv64 9.3.0-10ubuntu1 [6788 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 libstdc++-9-dev riscv64 9.3.0-10ubuntu1 [3649 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 libgcc-9-dev riscv64 9.3.0-10ubuntu1 [404 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 cpp-9 riscv64 9.3.0-10ubuntu1 [6046 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 gcc-9-base riscv64 9.3.0-10ubuntu1 [19.2 kB] Get:21 http://ftpmaster.internal/ubuntu focal/universe riscv64 gcc-8-base riscv64 8.4.0-3ubuntu2 [18.4 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 libperl5.30 riscv64 5.30.0-9build1 [3422 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.4 MB in 7s (5430 kB/s) (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_riscv64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu2) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../perl-base_5.30.0-9build1_riscv64.deb ... Unpacking perl-base (5.30.0-9build1) over (5.30.0-9build1) ... Setting up perl-base (5.30.0-9build1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.31-0ubuntu7_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Preparing to unpack .../libc-dev-bin_2.31-0ubuntu7_riscv64.deb ... Unpacking libc-dev-bin (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Preparing to unpack .../libc6_2.31-0ubuntu7_riscv64.deb ... Unpacking libc6:riscv64 (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Setting up libc6:riscv64 (2.31-0ubuntu7) ... 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Setting up libapt-pkg6.0:riscv64 (2.0.1ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.13-2ubuntu1_riscv64.deb ... Unpacking libgnutls30:riscv64 (3.6.13-2ubuntu1) over (3.6.11.1-2ubuntu2) ... Setting up libgnutls30:riscv64 (3.6.13-2ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../apt_2.0.1ubuntu1_riscv64.deb ... Unpacking apt (2.0.1ubuntu1) over (2.0.1) ... Setting up apt (2.0.1ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-4_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-4) over (1.07-4) ... Preparing to unpack .../01-libtext-charwidth-perl_0.04-10_riscv64.deb ... Unpacking libtext-charwidth-perl (0.04-10) over (0.04-10) ... Preparing to unpack .../02-libtext-iconv-perl_1.7-7_riscv64.deb ... Unpacking libtext-iconv-perl (1.7-7) over (1.7-7) ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19100189 riscv64 focal -c chroot:build-PACKAGEBUILD-19100189 --arch=riscv64 --dist=focal --nolog augustus_3.3.3+dfsg-2build1.dsc Initiating build PACKAGEBUILD-19100189 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-047 +==============================================================================+ | augustus 3.3.3+dfsg-2build1 (riscv64) Mon, 06 Apr 2020 12:05:31 +0000 | +==============================================================================+ Package: augustus Version: 3.3.3+dfsg-2build1 Source Version: 3.3.3+dfsg-2build1 Distribution: focal Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19100189/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-RRhtFE/resolver-nDrk5B' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- augustus_3.3.3+dfsg-2build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/augustus-RRhtFE/augustus-3.3.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-RRhtFE' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 12), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libcurl4-nss-dev, libssl-dev, asciidoctor, build-essential, fakeroot Filtered Build-Depends: debhelper (>= 12), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libcurl4-nss-dev, libssl-dev, asciidoctor, build-essential, fakeroot 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 [449 B] Get:5 copy:/<>/apt_archive ./ Packages [536 B] Fetched 1942 B in 0s (4649 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl libasn1-8-heimdal libbam-dev libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.71-dev libboost-iostreams1.71.0 libboost-regex1.71-dev libboost-regex1.71.0 libboost1.71-dev libbrotli1 libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcurl3-nss libcurl4-nss-dev libcxsparse3 libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgraphblas3 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu-dev libicu66 libk5crypto3 libkeyutils1 libklu1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libldap-common libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmetis5 libmongoose2 libncurses-dev libncurses5-dev libncurses6 libnghttp2-14 libnspr4 libnss3 libpipeline1 libpsl5 librbio2 libroken18-heimdal librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libspqr2 libsqlite3-dev libssh-4 libssl-dev libsub-override-perl libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5 libwind0-heimdal libxml2 libyaml-0-2 lzma-dev m4 man-db po-debconf rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc liblapack-doc libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-serialization1.71-dev libboost-stacktrace1.71-dev libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev libnss3-dev librtmp-dev libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user icu-doc liblzma-doc ncurses-doc sqlite3-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl ri ruby-dev bundler Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl libasn1-8-heimdal libbam-dev libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.71-dev libboost-iostreams1.71.0 libboost-regex1.71-dev libboost-regex1.71.0 libboost1.71-dev libbrotli1 libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcurl3-nss libcurl4-nss-dev libcxsparse3 libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgraphblas3 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu-dev libicu66 libk5crypto3 libkeyutils1 libklu1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libldap-common libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmetis5 libmongoose2 libncurses-dev libncurses5-dev libncurses6 libnghttp2-14 libnspr4 libnss3 libpipeline1 libpsl5 librbio2 libroken18-heimdal librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libspqr2 libsqlite3-dev libssh-4 libssl-dev libsub-override-perl libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5 libwind0-heimdal libxml2 libyaml-0-2 lzma-dev m4 man-db po-debconf rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration sbuild-build-depends-main-dummy tzdata zlib1g-dev 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 110 MB of archives. After this operation, 1089 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [960 B] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 libbsd0 riscv64 0.10.0-1 [42.0 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libruby2.7 riscv64 2.7.0-4+riscv64.1 [3322 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 bsdmainutils riscv64 11.1.2ubuntu3 [176 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libuchardet0 riscv64 0.0.6-3build1 [64.9 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 groff-base riscv64 1.22.4-4build1 [816 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 libpipeline1 riscv64 1.5.2-2build1 [23.9 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main riscv64 man-db riscv64 2.9.1-1 [1075 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main riscv64 libncurses6 riscv64 6.2-0ubuntu2 [86.2 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic-mgc riscv64 1:5.38-4 [218 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic1 riscv64 1:5.38-4 [70.5 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 file riscv64 1:5.38-4 [22.5 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 libelf1 riscv64 0.176-1.1build1 [41.8 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 libglib2.0-0 riscv64 2.64.1-1 [1122 kB] Get:15 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 ruby2.7 riscv64 2.7.0-4+riscv64.1 [95.4 kB] Get:16 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libldap-2.4-2 riscv64 2.4.49+dfsg-2ubuntu1 [137 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 tzdata all 2019c-3ubuntu1 [294 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu66 riscv64 66.1-2ubuntu2 [8406 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 libxml2 riscv64 2.9.10+dfsg-4build1 [558 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 libyaml-0-2 riscv64 0.2.2-1 [45.7 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext-base riscv64 0.19.8.1-10build1 [47.4 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5support0 riscv64 1.17-6ubuntu4 [28.3 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main riscv64 libk5crypto3 riscv64 1.17-6ubuntu4 [91.8 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main riscv64 libkeyutils1 riscv64 1.6-6ubuntu1 [9316 B] Get:25 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5-3 riscv64 1.17-6ubuntu4 [295 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main riscv64 libgssapi-krb5-2 riscv64 1.17-6ubuntu4 [107 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main riscv64 libpsl5 riscv64 0.21.0-1ubuntu1 [50.5 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main riscv64 rubygems-integration all 1.16 [5092 B] Get:29 http://ftpmaster.internal/ubuntu focal/main riscv64 rake all 13.0.1-2 [45.2 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main riscv64 ruby-did-you-mean all 1.2.1-1 [9828 B] Get:31 http://ftpmaster.internal/ubuntu focal/main riscv64 ruby-minitest all 5.13.0-1 [40.9 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main riscv64 ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main riscv64 ruby-power-assert all 1.1.7-1 [11.4 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main riscv64 ruby-test-unit all 3.3.4-1 [73.1 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main riscv64 ruby-xmlrpc all 0.3.0-2 [23.8 kB] Get:36 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 ruby riscv64 1:2.7 [5380 B] Get:37 http://ftpmaster.internal/ubuntu focal/universe riscv64 ruby-asciidoctor all 2.0.10-2 [166 kB] Get:38 http://ftpmaster.internal/ubuntu focal/universe riscv64 asciidoctor all 2.0.10-2 [40.3 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main riscv64 libsigsegv2 riscv64 2.12-2 [13.0 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main riscv64 m4 riscv64 1.4.18-4 [188 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main riscv64 autoconf all 2.69-11.1 [321 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main riscv64 autotools-dev all 20180224.1 [39.6 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main riscv64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main riscv64 autopoint all 0.19.8.1-10build1 [412 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main riscv64 libtool all 2.4.6-13 [161 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-autoreconf all 19 [16.1 kB] Get:47 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main riscv64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:50 http://ftpmaster.internal/ubuntu focal/main riscv64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:52 http://ftpmaster.internal/ubuntu focal/main riscv64 dwz riscv64 0.13-5 [147 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main riscv64 libcroco3 riscv64 0.6.13-1 [71.1 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext riscv64 0.19.8.1-10build1 [844 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main riscv64 po-debconf all 1.0.21 [233 kB] Get:57 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 debhelper all 12.10ubuntu1 [877 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main riscv64 icu-devtools riscv64 66.1-2ubuntu2 [177 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main riscv64 libsuitesparseconfig5 riscv64 1:5.7.1+dfsg-2 [9288 B] Get:60 http://ftpmaster.internal/ubuntu focal/main riscv64 libamd2 riscv64 1:5.7.1+dfsg-2 [18.3 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main riscv64 libroken18-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [36.5 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main riscv64 libasn1-8-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [145 kB] Get:63 http://ftpmaster.internal/ubuntu focal/universe riscv64 libbam-dev riscv64 0.1.19-4 [230 kB] Get:64 http://ftpmaster.internal/ubuntu focal/universe riscv64 libbamtools2.5.1 riscv64 2.5.1+dfsg-5build1 [151 kB] Get:65 http://ftpmaster.internal/ubuntu focal/universe riscv64 libbamtools-dev riscv64 2.5.1+dfsg-5build1 [19.8 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main riscv64 libblas3 riscv64 3.9.0-1build1 [106 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main riscv64 libblas-dev riscv64 3.9.0-1build1 [226 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main riscv64 libboost1.71-dev riscv64 1.71.0-6ubuntu6 [9068 kB] Get:69 http://ftpmaster.internal/ubuntu focal/universe riscv64 libboost-regex1.71.0 riscv64 1.71.0-6ubuntu6 [452 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu-dev riscv64 66.1-2ubuntu2 [12.5 MB] Get:71 http://ftpmaster.internal/ubuntu focal/universe riscv64 libboost-regex1.71-dev riscv64 1.71.0-6ubuntu6 [1604 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main riscv64 libboost-iostreams1.71.0 riscv64 1.71.0-6ubuntu6 [234 kB] Get:73 http://ftpmaster.internal/ubuntu focal/universe riscv64 libboost-iostreams1.71-dev riscv64 1.71.0-6ubuntu6 [340 kB] Get:74 http://ftpmaster.internal/ubuntu focal/universe riscv64 libboost-iostreams-dev riscv64 1.71.0.0ubuntu1 [3384 B] Get:75 http://ftpmaster.internal/ubuntu focal/main riscv64 libbrotli1 riscv64 1.0.7-6build1 [279 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main riscv64 libbtf1 riscv64 1:5.7.1+dfsg-2 [10.9 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main riscv64 libbz2-dev riscv64 1.0.8-2 [67.0 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main riscv64 libcamd2 riscv64 1:5.7.1+dfsg-2 [19.5 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main riscv64 libccolamd2 riscv64 1:5.7.1+dfsg-2 [20.6 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main riscv64 libcolamd2 riscv64 1:5.7.1+dfsg-2 [15.1 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main riscv64 libgfortran5 riscv64 10-20200324-1ubuntu1 [329 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main riscv64 liblapack3 riscv64 3.9.0-1build1 [1669 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main riscv64 libmetis5 riscv64 5.1.0.dfsg-5 [142 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main riscv64 libcholmod3 riscv64 1:5.7.1+dfsg-2 [293 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main riscv64 libheimbase1-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [24.7 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main riscv64 libhcrypto4-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [86.5 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main riscv64 libwind0-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [47.0 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main riscv64 libhx509-5-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [90.1 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5-26-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [175 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main riscv64 libheimntlm0-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [13.4 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main riscv64 libgssapi3-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [83.3 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main riscv64 libsasl2-modules-db riscv64 2.1.27+dfsg-2 [13.7 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main riscv64 libsasl2-2 riscv64 2.1.27+dfsg-2 [45.2 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main riscv64 libldap-common all 2.4.49+dfsg-2ubuntu1 [17.3 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main riscv64 libnghttp2-14 riscv64 1.40.0-1build1 [70.9 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build1 [50.8 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main riscv64 libssh-4 riscv64 0.9.3-2ubuntu1 [147 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main riscv64 libcurl3-gnutls riscv64 7.68.0-1ubuntu1 [205 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main riscv64 libnspr4 riscv64 2:4.25-1 [91.0 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main riscv64 libnss3 riscv64 2:3.49.1-1ubuntu1 [1041 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main riscv64 libcurl3-nss riscv64 7.68.0-1ubuntu1 [213 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main riscv64 libcurl4-nss-dev riscv64 7.68.0-1ubuntu1 [621 kB] Get:103 http://ftpmaster.internal/ubuntu focal/main riscv64 libcxsparse3 riscv64 1:5.7.1+dfsg-2 [59.3 kB] Get:104 http://ftpmaster.internal/ubuntu focal/universe riscv64 libdeflate0 riscv64 1.5-3 [52.1 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main riscv64 libgraphblas3 riscv64 1:5.7.1+dfsg-2 [3613 kB] Get:106 http://ftpmaster.internal/ubuntu focal/universe riscv64 libgslcblas0 riscv64 2.5+dfsg-6build1 [69.1 kB] Get:107 http://ftpmaster.internal/ubuntu focal/universe riscv64 libgsl23 riscv64 2.5+dfsg-6build1 [818 kB] Get:108 http://ftpmaster.internal/ubuntu focal/universe riscv64 libgsl-dev riscv64 2.5+dfsg-6build1 [2516 kB] Get:109 http://ftpmaster.internal/ubuntu focal/universe riscv64 libhts3 riscv64 1.10.2-3 [328 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main riscv64 liblzma-dev riscv64 5.2.4-1 [226 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main riscv64 zlib1g-dev riscv64 1:1.2.11.dfsg-2ubuntu1 [207 kB] Get:112 http://ftpmaster.internal/ubuntu focal/universe riscv64 libhts-dev riscv64 1.10.2-3 [92.0 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main riscv64 libklu1 riscv64 1:5.7.1+dfsg-2 [64.8 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main riscv64 liblapack-dev riscv64 3.9.0-1build1 [8476 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main riscv64 libldl2 riscv64 1:5.7.1+dfsg-2 [10.7 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main riscv64 libmongoose2 riscv64 1:5.7.1+dfsg-2 [31.1 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main riscv64 libumfpack5 riscv64 1:5.7.1+dfsg-2 [205 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main riscv64 librbio2 riscv64 1:5.7.1+dfsg-2 [22.0 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main riscv64 libspqr2 riscv64 1:5.7.1+dfsg-2 [58.4 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main riscv64 libsuitesparse-dev riscv64 1:5.7.1+dfsg-2 [34.8 MB] Get:121 http://ftpmaster.internal/ubuntu focal/main riscv64 liblpsolve55-dev riscv64 5.5.0.15-4build1 [545 kB] Get:122 http://ftpmaster.internal/ubuntu focal/main riscv64 libncurses-dev riscv64 6.2-0ubuntu2 [696 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main riscv64 libncurses5-dev riscv64 6.2-0ubuntu2 [980 B] Get:124 http://ftpmaster.internal/ubuntu focal/main riscv64 libsqlite3-dev riscv64 3.31.1-4 [1408 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main riscv64 libssl-dev riscv64 1.1.1d-2ubuntu6 [2519 kB] Get:126 http://ftpmaster.internal/ubuntu focal/universe riscv64 lzma-dev all 9.22-2.1build1 [41.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 110 MB in 23s (4719 kB/s) Selecting previously unselected package libbsd0:riscv64. (Reading database ... 9816 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_riscv64.deb ... Unpacking libbsd0:riscv64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2ubuntu3_riscv64.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../002-libuchardet0_0.0.6-3build1_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.6-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-4build1_riscv64.deb ... Unpacking groff-base (1.22.4-4build1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../004-libpipeline1_1.5.2-2build1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.1-1_riscv64.deb ... Unpacking man-db (2.9.1-1) ... Selecting previously unselected package libncurses6:riscv64. Preparing to unpack .../006-libncurses6_6.2-0ubuntu2_riscv64.deb ... Unpacking libncurses6:riscv64 (6.2-0ubuntu2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.38-4_riscv64.deb ... Unpacking libmagic-mgc (1:5.38-4) ... Selecting previously unselected package libmagic1:riscv64. Preparing to unpack .../008-libmagic1_1%3a5.38-4_riscv64.deb ... Unpacking libmagic1:riscv64 (1:5.38-4) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.38-4_riscv64.deb ... Unpacking file (1:5.38-4) ... Selecting previously unselected package libelf1:riscv64. Preparing to unpack .../010-libelf1_0.176-1.1build1_riscv64.deb ... Unpacking libelf1:riscv64 (0.176-1.1build1) ... Selecting previously unselected package libglib2.0-0:riscv64. Preparing to unpack .../011-libglib2.0-0_2.64.1-1_riscv64.deb ... Unpacking libglib2.0-0:riscv64 (2.64.1-1) ... Selecting previously unselected package tzdata. Preparing to unpack .../012-tzdata_2019c-3ubuntu1_all.deb ... Unpacking tzdata (2019c-3ubuntu1) ... Selecting previously unselected package libicu66:riscv64. Preparing to unpack .../013-libicu66_66.1-2ubuntu2_riscv64.deb ... Unpacking libicu66:riscv64 (66.1-2ubuntu2) ... Selecting previously unselected package libxml2:riscv64. Preparing to unpack .../014-libxml2_2.9.10+dfsg-4build1_riscv64.deb ... Unpacking libxml2:riscv64 (2.9.10+dfsg-4build1) ... Selecting previously unselected package libyaml-0-2:riscv64. Preparing to unpack .../015-libyaml-0-2_0.2.2-1_riscv64.deb ... Unpacking libyaml-0-2:riscv64 (0.2.2-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../016-gettext-base_0.19.8.1-10build1_riscv64.deb ... Unpacking gettext-base (0.19.8.1-10build1) ... Selecting previously unselected package libkrb5support0:riscv64. Preparing to unpack .../017-libkrb5support0_1.17-6ubuntu4_riscv64.deb ... Unpacking libkrb5support0:riscv64 (1.17-6ubuntu4) ... Selecting previously unselected package libk5crypto3:riscv64. Preparing to unpack .../018-libk5crypto3_1.17-6ubuntu4_riscv64.deb ... Unpacking libk5crypto3:riscv64 (1.17-6ubuntu4) ... Selecting previously unselected package libkeyutils1:riscv64. Preparing to unpack .../019-libkeyutils1_1.6-6ubuntu1_riscv64.deb ... Unpacking libkeyutils1:riscv64 (1.6-6ubuntu1) ... Selecting previously unselected package libkrb5-3:riscv64. Preparing to unpack .../020-libkrb5-3_1.17-6ubuntu4_riscv64.deb ... Unpacking libkrb5-3:riscv64 (1.17-6ubuntu4) ... Selecting previously unselected package libgssapi-krb5-2:riscv64. Preparing to unpack .../021-libgssapi-krb5-2_1.17-6ubuntu4_riscv64.deb ... Unpacking libgssapi-krb5-2:riscv64 (1.17-6ubuntu4) ... Selecting previously unselected package libpsl5:riscv64. Preparing to unpack .../022-libpsl5_0.21.0-1ubuntu1_riscv64.deb ... Unpacking libpsl5:riscv64 (0.21.0-1ubuntu1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../023-rubygems-integration_1.16_all.deb ... Unpacking rubygems-integration (1.16) ... Selecting previously unselected package rake. Preparing to unpack .../024-rake_13.0.1-2_all.deb ... Unpacking rake (13.0.1-2) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../025-ruby-did-you-mean_1.2.1-1_all.deb ... Unpacking ruby-did-you-mean (1.2.1-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../026-ruby-minitest_5.13.0-1_all.deb ... Unpacking ruby-minitest (5.13.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../027-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../028-ruby-power-assert_1.1.7-1_all.deb ... Unpacking ruby-power-assert (1.1.7-1) ... 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Setting up libnghttp2-14:riscv64 (1.40.0-1build1) ... Setting up libmagic1:riscv64 (1:5.38-4) ... Setting up libdeflate0 (1.5-3) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up rubygems-integration (1.16) ... Setting up libmetis5:riscv64 (5.1.0.dfsg-5) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu1) ... Setting up libboost-iostreams1.71.0:riscv64 (1.71.0-6ubuntu6) ... Setting up libbtf1:riscv64 (1:5.7.1+dfsg-2) ... Setting up libkrb5support0:riscv64 (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:riscv64 (2.1.27+dfsg-2) ... Setting up tzdata (2019c-3ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 6 12:12:32 UTC 2020. Universal Time is now: Mon Apr 6 12:12:32 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:riscv64 (3.9.0-1build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/riscv64-linux-gnu/libblas.so.3 (libblas.so.3-riscv64-linux-gnu) in auto mode Setting up libsqlite3-dev:riscv64 (3.31.1-4) ... Setting up ruby-test-unit (3.3.4-1) ... Setting up libnspr4:riscv64 (2:4.25-1) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libgsl23:riscv64 (2.5+dfsg-6build1) ... Setting up libncurses6:riscv64 (6.2-0ubuntu2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:riscv64 (2.12-2) ... Setting up libbamtools2.5.1:riscv64 (2.5.1+dfsg-5build1) ... Setting up libssl-dev:riscv64 (1.1.1d-2ubuntu6) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libbam-dev (0.1.19-4) ... Setting up libk5crypto3:riscv64 (1.17-6ubuntu4) ... Setting up libsasl2-2:riscv64 (2.1.27+dfsg-2) ... Setting up libgfortran5:riscv64 (10-20200324-1ubuntu1) ... Setting up libroken18-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up liblzma-dev:riscv64 (5.2.4-1) ... Setting up zlib1g-dev:riscv64 (1:1.2.11.dfsg-2ubuntu1) ... Setting up libuchardet0:riscv64 (0.0.6-3build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libcxsparse3:riscv64 (1:5.7.1+dfsg-2) ... Setting up libkrb5-3:riscv64 (1.17-6ubuntu4) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libbsd0:riscv64 (0.10.0-1) ... Setting up libelf1:riscv64 (0.176-1.1build1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libsuitesparseconfig5:riscv64 (1:5.7.1+dfsg-2) ... Setting up libblas-dev:riscv64 (3.9.0-1build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so to provide /usr/lib/riscv64-linux-gnu/libblas.so (libblas.so-riscv64-linux-gnu) in auto mode Setting up librbio2:riscv64 (1:5.7.1+dfsg-2) ... Setting up libheimbase1-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libbz2-dev:riscv64 (1.0.8-2) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libamd2:riscv64 (1:5.7.1+dfsg-2) ... Setting up liblapack3:riscv64 (3.9.0-1build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/riscv64-linux-gnu/liblapack.so.3 (liblapack.so.3-riscv64-linux-gnu) in auto mode Setting up libncurses-dev:riscv64 (6.2-0ubuntu2) ... Setting up libgsl-dev (2.5+dfsg-6build1) ... Setting up libcolamd2:riscv64 (1:5.7.1+dfsg-2) ... Setting up libtool (2.4.6-13) ... Setting up libicu66:riscv64 (66.1-2ubuntu2) ... Setting up libasn1-8-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up m4 (1.4.18-4) ... Setting up libnss3:riscv64 (2:3.49.1-1ubuntu1) ... Setting up libhcrypto4-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libcamd2:riscv64 (1:5.7.1+dfsg-2) ... Setting up libmongoose2:riscv64 (1:5.7.1+dfsg-2) ... Setting up libwind0-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libbamtools-dev:riscv64 (2.5.1+dfsg-5build1) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up liblapack-dev:riscv64 (3.9.0-1build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so to provide /usr/lib/riscv64-linux-gnu/liblapack.so (liblapack.so-riscv64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:riscv64 (1.17-6ubuntu4) ... Setting up icu-devtools (66.1-2ubuntu2) ... Setting up libboost-regex1.71.0:riscv64 (1.71.0-6ubuntu6) ... Setting up libssh-4:riscv64 (0.9.3-2ubuntu1) ... Setting up lzma-dev (9.22-2.1build1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4build1) ... Setting up libklu1:riscv64 (1:5.7.1+dfsg-2) ... Setting up libccolamd2:riscv64 (1:5.7.1+dfsg-2) ... Setting up libncurses5-dev:riscv64 (6.2-0ubuntu2) ... Setting up libicu-dev:riscv64 (66.1-2ubuntu2) ... Setting up libxml2:riscv64 (2.9.10+dfsg-4build1) ... Setting up libcholmod3:riscv64 (1:5.7.1+dfsg-2) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libspqr2:riscv64 (1:5.7.1+dfsg-2) ... Setting up libhx509-5-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libumfpack5:riscv64 (1:5.7.1+dfsg-2) ... Setting up libboost-regex1.71-dev:riscv64 (1.71.0-6ubuntu6) ... Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up libboost-iostreams1.71-dev:riscv64 (1.71.0-6ubuntu6) ... Setting up libkrb5-26-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libsuitesparse-dev:riscv64 (1:5.7.1+dfsg-2) ... Setting up libboost-iostreams-dev:riscv64 (1.71.0.0ubuntu1) ... Setting up libheimntlm0-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgssapi3-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up liblpsolve55-dev (5.5.0.15-4build1) ... Setting up po-debconf (1.0.21) ... Setting up libldap-2.4-2:riscv64 (2.4.49+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:riscv64 (7.68.0-1ubuntu1) ... Setting up libcurl3-nss:riscv64 (7.68.0-1ubuntu1) ... Setting up libcurl4-nss-dev:riscv64 (7.68.0-1ubuntu1) ... Setting up libhts3:riscv64 (1.10.2-3) ... Setting up libhts-dev:riscv64 (1.10.2-3) ... Setting up rake (13.0.1-2) ... Setting up debhelper (12.10ubuntu1) ... Setting up libruby2.7:riscv64 (2.7.0-4+riscv64.1) ... Setting up dh-autoreconf (19) ... Setting up ruby2.7 (2.7.0-4+riscv64.1) ... Setting up ruby (1:2.7) ... Setting up ruby-asciidoctor (2.0.10-2) ... Setting up asciidoctor (2.0.10-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 (riscv64) Toolchain package versions: binutils_2.34-5ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-10ubuntu1 gcc-9_9.3.0-10ubuntu1 libc6-dev_2.31-0ubuntu7 libstdc++-9-dev_9.3.0-10ubuntu1 libstdc++6_10-20200324-1ubuntu1 linux-libc-dev_5.4.0-21.25 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.1ubuntu1 asciidoctor_2.0.10-2 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu4 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-5ubuntu1 binutils-common_2.34-5ubuntu1 binutils-riscv64-linux-gnu_2.34-5ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu8 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-10ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 file_1:5.38-4 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-10ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200324-1ubuntu1 gcc-8-base_8.4.0-3ubuntu2 gcc-9_9.3.0-10ubuntu1 gcc-9-base_9.3.0-10ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 hostname_3.23 icu-devtools_66.1-2ubuntu2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libamd2_1:5.7.1+dfsg-2 libapt-pkg6.0_2.0.1ubuntu1 libarchive-zip-perl_1.67-2 libasn1-8-heimdal_7.7.0+dfsg-1ubuntu1 libassuan0_2.5.3-7ubuntu2 libatomic1_10-20200324-1ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbam-dev_0.1.19-4 libbamtools-dev_2.5.1+dfsg-5build1 libbamtools2.5.1_2.5.1+dfsg-5build1 libbinutils_2.34-5ubuntu1 libblas-dev_3.9.0-1build1 libblas3_3.9.0-1build1 libblkid1_2.34-0.1ubuntu8 libboost-iostreams-dev_1.71.0.0ubuntu1 libboost-iostreams1.71-dev_1.71.0-6ubuntu6 libboost-iostreams1.71.0_1.71.0-6ubuntu6 libboost-regex1.71-dev_1.71.0-6ubuntu6 libboost-regex1.71.0_1.71.0-6ubuntu6 libboost1.71-dev_1.71.0-6ubuntu6 libbrotli1_1.0.7-6build1 libbsd0_0.10.0-1 libbtf1_1:5.7.1+dfsg-2 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.31-0ubuntu7 libc-dev-bin_2.31-0ubuntu7 libc6_2.31-0ubuntu7 libc6-dev_2.31-0ubuntu7 libcamd2_1:5.7.1+dfsg-2 libcap-ng0_0.7.9-2.1build1 libcc1-0_10-20200324-1ubuntu1 libccolamd2_1:5.7.1+dfsg-2 libcholmod3_1:5.7.1+dfsg-2 libcolamd2_1:5.7.1+dfsg-2 libcom-err2_1.45.5-2ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10ubuntu4 libcrypt1_1:4.4.10-10ubuntu4 libctf-nobfd0_2.34-5ubuntu1 libctf0_2.34-5ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu1 libcurl3-nss_7.68.0-1ubuntu1 libcurl4-nss-dev_7.68.0-1ubuntu1 libcxsparse3_1:5.7.1+dfsg-2 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_12.10ubuntu1 libdeflate0_1.5-3 libdpkg-perl_1.19.7ubuntu3 libelf1_0.176-1.1build1 libext2fs2_1.45.5-2ubuntu1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.3.0-10ubuntu1 libgcc-s1_10-20200324-1ubuntu1 libgcc1_1:10-20200324-1ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10-20200324-1ubuntu1 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2ubuntu1 libgomp1_10-20200324-1ubuntu1 libgpg-error0_1.37-1 libgpm2_1.20.7-5 libgraphblas3_1:5.7.1+dfsg-2 libgsl-dev_2.5+dfsg-6build1 libgsl23_2.5+dfsg-6build1 libgslcblas0_2.5+dfsg-6build1 libgssapi-krb5-2_1.17-6ubuntu4 libgssapi3-heimdal_7.7.0+dfsg-1ubuntu1 libhcrypto4-heimdal_7.7.0+dfsg-1ubuntu1 libheimbase1-heimdal_7.7.0+dfsg-1ubuntu1 libheimntlm0-heimdal_7.7.0+dfsg-1ubuntu1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libhx509-5-heimdal_7.7.0+dfsg-1ubuntu1 libicu-dev_66.1-2ubuntu2 libicu66_66.1-2ubuntu2 libidn2-0_2.2.0-2 libisl22_0.22.1-1 libk5crypto3_1.17-6ubuntu4 libkeyutils1_1.6-6ubuntu1 libklu1_1:5.7.1+dfsg-2 libkrb5-26-heimdal_7.7.0+dfsg-1ubuntu1 libkrb5-3_1.17-6ubuntu4 libkrb5support0_1.17-6ubuntu4 liblapack-dev_3.9.0-1build1 liblapack3_3.9.0-1build1 libldap-2.4-2_2.4.49+dfsg-2ubuntu1 libldap-common_2.4.49+dfsg-2ubuntu1 libldl2_1:5.7.1+dfsg-2 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblpsolve55-dev_5.5.0.15-4build1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmetis5_5.1.0.dfsg-5 libmongoose2_1:5.7.1+dfsg-2 libmount1_2.34-0.1ubuntu8 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.2-0ubuntu2 libncurses5-dev_6.2-0ubuntu2 libncurses6_6.2-0ubuntu2 libncursesw6_6.2-0ubuntu2 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1build1 libnpth0_1.6-1 libnspr4_2:4.25-1 libnss3_2:3.49.1-1ubuntu1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.0-9build1 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libpsl5_0.21.0-1ubuntu1 librbio2_1:5.7.1+dfsg-2 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-1ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libruby2.7_2.7.0-4+riscv64.1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu8 libspqr2_1:5.7.1+dfsg-2 libsqlite3-0_3.31.1-4 libsqlite3-dev_3.31.1-4 libss2_1.45.5-2ubuntu1 libssh-4_0.9.3-2ubuntu1 libssl-dev_1.1.1d-2ubuntu6 libssl1.1_1.1.1d-2ubuntu6 libstdc++-9-dev_9.3.0-10ubuntu1 libstdc++6_10-20200324-1ubuntu1 libsub-override-perl_0.09-2 libsuitesparse-dev_1:5.7.1+dfsg-2 libsuitesparseconfig5_1:5.7.1+dfsg-2 libsystemd0_245.2-1ubuntu3 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-0ubuntu2 libtool_2.4.6-13 libuchardet0_0.0.6-3build1 libudev1_245.2-1ubuntu3 libumfpack5_1:5.7.1+dfsg-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu8 libwind0-heimdal_7.7.0+dfsg-1ubuntu1 libxml2_2.9.10+dfsg-4build1 libyaml-0-2_0.2.2-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-21.25 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu3 logsave_1.45.5-2ubuntu1 lsb-base_11.1.0ubuntu2 lzma-dev_9.22-2.1build1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1ubuntu8 ncurses-base_6.2-0ubuntu2 ncurses-bin_6.2-0ubuntu2 openssl_1.1.1d-2ubuntu6 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu3 patch_2.7.6-6 perl_5.30.0-9build1 perl-base_5.30.0-9build1 perl-modules-5.30_5.30.0-9build1 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 rake_13.0.1-2 readline-common_8.0-4 ruby_1:2.7 ruby-asciidoctor_2.0.10-2 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-1 ruby-test-unit_3.3.4-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.0-4+riscv64.1 rubygems-integration_1.16 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1ubuntu1 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 util-linux_2.34-0.1ubuntu8 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: augustus Binary: augustus, augustus-data, augustus-doc Architecture: any all Version: 3.3.3+dfsg-2build1 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: http://bioinf.uni-greifswald.de/augustus/ Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/augustus Vcs-Git: https://salsa.debian.org/med-team/augustus.git Testsuite: autopkgtest Build-Depends: debhelper (>= 12), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libcurl4-nss-dev, libssl-dev, asciidoctor Package-List: augustus deb science optional arch=any augustus-data deb science optional arch=all augustus-doc deb doc optional arch=all Checksums-Sha1: 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dpkg-source: info: applying set_installdir dpkg-source: info: applying keep_cflags dpkg-source: info: applying buildflags.patch dpkg-source: info: applying interpreter_paths.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19100189 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19100189 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19100189 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.3.3+dfsg-2build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/<>/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/<>/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/<>/auxprogs/homGeneMapping' (cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping) make[3]: Entering directory '/<>/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o make[3]: Leaving directory '/<>/auxprogs/homGeneMapping/src' /bin/sh: 1: cd: can't cd to ../bin /bin/sh: 1: cd: can't cd to ../../../bin make[2]: Leaving directory '/<>/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/<>/auxprogs/joingenes' rm -rf *o joingenes; rm -rf ../../bin/joingenes make[2]: Leaving directory '/<>/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/<>/auxprogs/aln2wig' rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig make[2]: Leaving directory '/<>/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/<>/auxprogs/bam2wig' rm -f bam2wig bam2wig.o rm -f ../../bin/bam2wig make[2]: Leaving directory '/<>/auxprogs/bam2wig' /usr/bin/make -C auxprogs/checkTargetSortedness clean make[2]: Entering directory '/<>/auxprogs/checkTargetSortedness' rm -f *.o checkTargetSortedness make[2]: Leaving directory '/<>/auxprogs/checkTargetSortedness' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/<>/auxprogs/compileSpliceCands' rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o make[2]: Leaving directory '/<>/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/<>/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/<>/auxprogs/filterBam/src' rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o rm -f ../../../bin/filterBam make[3]: Leaving directory '/<>/auxprogs/filterBam/src' make[2]: Leaving directory '/<>/auxprogs/filterBam' rm -rf bin rm -f debian/*substvars make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/<>/auxprogs/aln2wig' gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c aln2wig.c In file included from /usr/include/string.h:495, from aln2wig.c:15: In function ‘strncpy’, inlined from ‘main’ at aln2wig.c:454:6: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘main’ at aln2wig.c:460:6: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘main’ at aln2wig.c:327:6: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘main’ at aln2wig.c:334:6: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o; cp aln2wig ../../bin make[2]: Leaving directory '/<>/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/<>/auxprogs/bam2hints' g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz mkdir -p ../../bin cp bam2hints ../../bin make[2]: Leaving directory '/<>/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/<>/auxprogs/bam2wig' cc -Wall -O2 -I/usr/include/samtools -I. -I/usr/include/htslib -I/usr/include/bcftools -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c bam2wig.c -o bam2wig.o cc -Wall -O2 -I/usr/include/samtools -I. -I/usr/include/htslib -I/usr/include/bcftools -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig /usr/lib/libbam.a -lhts -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto -lbz2 -llzma mkdir -p ../../bin cp bam2wig ../../bin/bam2wig make[2]: Leaving directory '/<>/auxprogs/bam2wig' /usr/bin/make -C auxprogs/checkTargetSortedness make[2]: Entering directory '/<>/auxprogs/checkTargetSortedness' cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c checkTargetSortedness.c -o checkTargetSortedness.o -I/usr/include/samtools -I. cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now checkTargetSortedness.o -o checkTargetSortedness -lbam -lcurses -lm -lz -lpthread make[2]: Leaving directory '/<>/auxprogs/checkTargetSortedness' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/<>/auxprogs/compileSpliceCands' cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c In file included from /usr/include/string.h:495, from compileSpliceCands.c:12: In function ‘strncat’, inlined from ‘getChromosome’ at compileSpliceCands.c:216:2: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:136:10: warning: ‘__builtin_strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c: In function ‘getChromosome’: compileSpliceCands.c:216:2: note: length computed here 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from compileSpliceCands.c:12: In function ‘strncpy’, inlined from ‘parseLine’ at compileSpliceCands.c:292:2: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c: In function ‘parseList’: compileSpliceCands.c:344:35: warning: ‘left’ may be used uninitialized in this function [-Wmaybe-uninitialized] 344 | findPossibleSpliceSites(left->name,actualChromosome,left->startPos-maxSpliceSiteDiff,left->endPos+maxSpliceSiteDiff,right->startPos-maxSpliceSiteDiff,right->startPos+maxSpliceSiteDiff,left->strand,right->strand); | ~~~~^~~~~~ compileSpliceCands.c: In function ‘main’: compileSpliceCands.c:563:3: warning: ‘chromosomeLength’ may be used uninitialized in this function [-Wmaybe-uninitialized] 563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c cc -o compileSpliceCands compileSpliceCands.o list.o -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now; make[2]: Leaving directory '/<>/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/<>/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/<>/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/<>/auxprogs/filterBam/src' make[2]: Leaving directory '/<>/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/<>/auxprogs/homGeneMapping/src' g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gene.o gene.cc -I../include g++ -c -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o genome.o genome.cc -I../include g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o homGeneMapping main.cc gene.o genome.o -I../include mkdir -p ../../../bin/ cp homGeneMapping ../../../bin/homGeneMapping make[2]: Leaving directory '/<>/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/<>/auxprogs/joingenes' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_ios.cpp In file included from /usr/include/string.h:495, from jg_transcript.h:5, from jg_ios.cpp:1: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)’ at jg_ios.cpp:251:14: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)’ at jg_ios.cpp:79:14: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)’ at jg_ios.cpp:148:9: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 300 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.o jg_transcript.o jg_ios.o -o joingenes -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now cp joingenes ../../bin/ make[2]: Leaving directory '/<>/auxprogs/joingenes' dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>' mkdir -p bin cd src && make make[3]: Entering directory '/<>/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include In file included from /usr/include/string.h:495, from /usr/include/c++/9/cstring:42, from ../include/types.hh:18, from ../include/hints.hh:12, from hints.cc:10: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘std::istream& operator>>(std::istream&, Feature&)’ at hints.cc:82:9: /usr/include/riscv64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include exonmodel.cc: In static member function ‘static void ExonModel::readAllParameters()’: exonmodel.cc:671:28: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 671 | sprintf(zusString, "[%d]", idx+1); | ^~ exonmodel.cc:671:26: note: directive argument in the range [1, 2147483647] 671 | sprintf(zusString, "[%d]", idx+1); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from ../include/matrix.hh:13, from ../include/statemodel.hh:12, from ../include/exonmodel.hh:11, from exonmodel.cc:8: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ igenicmodel.cc: In static member function ‘static void IGenicModel::readAllParameters()’: igenicmodel.cc:162:25: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 162 | sprintf(zusString, "[%d]", idx+1); | ^~ igenicmodel.cc:162:23: note: directive argument in the range [1, 2147483647] 162 | sprintf(zusString, "[%d]", idx+1); | ^~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6493, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from ../include/matrix.hh:13, from ../include/statemodel.hh:12, from ../include/igenicmodel.hh:11, from igenicmodel.cc:10: /usr/include/riscv64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include echo "-Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security" > cxxflags g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o dummy.o -I../include cp prepareAlign ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o -I../include cp fastBlockSearch ../bin/ cp augustus ../bin/ cp etraining ../bin/ make[3]: Leaving directory '/<>/src' cd auxprogs && make make[3]: Entering directory '/<>/auxprogs' cd bam2hints; make; make[4]: Entering directory '/<>/auxprogs/bam2hints' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'bam2hints' is up to date. make[4]: Leaving directory '/<>/auxprogs/bam2hints' cd compileSpliceCands; make; make[4]: Entering directory '/<>/auxprogs/compileSpliceCands' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'compileSpliceCands' is up to date. make[4]: Leaving directory '/<>/auxprogs/compileSpliceCands' cd filterBam; make; make[4]: Entering directory '/<>/auxprogs/filterBam' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[5]: Entering directory '/<>/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mv filterBam ../../../bin/filterBam make[5]: Leaving directory '/<>/auxprogs/filterBam/src' make[4]: Leaving directory '/<>/auxprogs/filterBam' cd homGeneMapping; make; make[4]: Entering directory '/<>/auxprogs/homGeneMapping' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[5]: Entering directory '/<>/auxprogs/homGeneMapping/src' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/<>/auxprogs/homGeneMapping/src' make[4]: Leaving directory '/<>/auxprogs/homGeneMapping' cd joingenes; make; make[4]: Entering directory '/<>/auxprogs/joingenes' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/auxprogs/joingenes' cd bam2wig; make; make[4]: Entering directory '/<>/auxprogs/bam2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'bam2wig' is up to date. make[4]: Leaving directory '/<>/auxprogs/bam2wig' cd utrrnaseq/Debug; make all; make[4]: Entering directory '/<>/auxprogs/utrrnaseq/Debug' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Building file: ../src/Compute_UTRs.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp" Finished building: ../src/Compute_UTRs.cpp Building file: ../src/Coord_Transform.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp" Finished building: ../src/Coord_Transform.cpp Building file: ../src/Genomic_Data.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp" Finished building: ../src/Genomic_Data.cpp Building file: ../src/Splice_Sites.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp" Finished building: ../src/Splice_Sites.cpp Building file: ../src/Supporting_Methods.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp" Finished building: ../src/Supporting_Methods.cpp Building file: ../src/Test.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp" Finished building: ../src/Test.cpp Building file: ../src/UTRs.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp" Finished building: ../src/UTRs.cpp Building file: ../src/main.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp" Finished building: ../src/main.cpp Building target: utrrnaseq Invoking: GCC C++ Linker g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o Finished building target: utrrnaseq make[4]: Leaving directory '/<>/auxprogs/utrrnaseq/Debug' make[3]: Leaving directory '/<>/auxprogs' make[2]: Leaving directory '/<>' asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 test make[1]: Entering directory '/<>' cd src && make unittest make[2]: Entering directory '/<>/src' cd googletest && make make[3]: Entering directory '/<>/src/googletest' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -isystem ./include -I. -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wextra -pthread -std=c++11 -c \ ./src/gtest-all.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -isystem ./include -I. -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wextra -pthread -std=c++11 -c \ ./src/gtest_main.cc ar rv libgtest.a gtest-all.o ar rv libgtest_main.a gtest-all.o gtest_main.o ar: ar: creating libgtest.acreating libgtest_main.a a - gtest-all.o a - gtest-all.o a - gtest_main.o make[3]: Leaving directory '/<>/src/googletest' cd unittests && make make[3]: Entering directory '/<>/src/unittests' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -pedantic -pthread -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -L../googletest -lgtest -lgtest_main -I../../include -isystem ../googletest/include/ -c lldouble_unittest.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -pedantic -pthread -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -L../googletest -lgtest -lgtest_main -I../../include -isystem ../googletest/include/ -c fasta_unittest.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -pedantic -pthread -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -L../googletest -lgtest -lgtest_main -I../../include -isystem ../googletest/include/ lldouble_unittest.o fasta_unittest.o ../lldouble.o ../fasta.o -o unittests make[3]: Leaving directory '/<>/src/unittests' make[2]: Leaving directory '/<>/src' cd src/unittests && ./unittests Running main() from ./src/gtest_main.cc [==========] Running 4 tests from 2 test suites. [----------] Global test environment set-up. [----------] 3 tests from LLDoubleTest [ RUN ] LLDoubleTest.Summation [ OK ] LLDoubleTest.Summation (8 ms) [ RUN ] LLDoubleTest.SimpleMultiplication [ OK ] LLDoubleTest.SimpleMultiplication (1 ms) [ RUN ] LLDoubleTest.ChainMultiplication [ OK ] LLDoubleTest.ChainMultiplication (6 ms) [----------] 3 tests from LLDoubleTest (18 ms total) [----------] 1 test from FastaTest [ RUN ] FastaTest.ReadFile [ OK ] FastaTest.ReadFile (5 ms) [----------] 1 test from FastaTest (5 ms total) [----------] Global test environment tear-down [==========] 4 tests from 2 test suites ran. (34 ms total) [ PASSED ] 4 tests. ./bin/augustus --species=human --UTR=on examples/example.fa # This output was generated with AUGUSTUS (version 3.3.3). # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), # O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Initializing the parameters using config directory /<>/config/ ... # human version. Using species specific transition matrix: /<>/config/species/human/human_trans_shadow_partial_utr.pbl # Looks like examples/example.fa is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- # # Predicted genes for sequence number 1 on both strands # start gene g1 HS04636 AUGUSTUS gene 836 8857 1 + . g1 HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1"; HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1"; # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] # end gene g1 ### # # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- # # Predicted genes for sequence number 2 on both strands # start gene g2 HS08198 AUGUSTUS gene 86 2344 1 + . g2 HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1 HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2"; # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] # end gene g2 ### # command line: # ./bin/augustus --species=human --UTR=on examples/example.fa make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mkdir -p debian/augustus/usr/bin install bin/* debian/augustus/usr/bin install auxprogs/checkTargetSortedness/checkTargetSortedness \ debian/augustus/usr/bin install auxprogs/bam2wig/bam2wig \ debian/augustus/usr/bin install auxprogs/compileSpliceCands/compileSpliceCands \ debian/augustus/usr/bin install auxprogs/homGeneMapping/src/homGeneMapping \ debian/augustus/usr/bin install auxprogs/joingenes/joingenes \ debian/augustus/usr/bin mkdir -p debian/augustus/usr/share/augustus cp -r scripts debian/augustus/usr/share/augustus chmod -R -x debian/augustus/usr/share/augustus/scripts/* rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \ debian/augustus/usr/share/augustus/scripts/aln2wig chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \ debian/augustus/usr/share/augustus/scripts/*.pl* mkdir -p debian/augustus-doc/usr/share/doc/augustus cp README* debian/augustus-doc/usr/share/doc/augustus cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial \ debian/augustus-doc/usr/share/doc/augustus mkdir -p debian/augustus-data/usr/share/augustus cp -r config debian/augustus-data/usr/share/augustus find debian/augustus-data/usr/share/augustus \ -type f -exec chmod -x {} \; make[1]: Leaving directory '/<>' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs -k HISTORY.TXT make[1]: Leaving directory '/<>' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress -Xtutorial make[1]: Leaving directory '/<>' dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a debian/rules override_dh_gencontrol make[1]: Entering directory '/<>' echo "libbam-dev:Version=0.1.19-4" >> debian/augustus.substvars dh_gencontrol dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined make[1]: Leaving directory '/<>' dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing augustus (in debian/augustus); do_strip: , oemstrip: pkgstriptranslations: processing augustus-dbgsym (in debian/.debhelper/augustus/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/augustus/DEBIAN/control, package augustus, directory debian/augustus .. removing usr/share/doc/augustus/changelog.gz pkgstripfiles: Truncating usr/share/doc/augustus/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package augustus ... pkgstripfiles: No PNG files. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " dpkg-deb: building package 'augustus' in '../augustus_3.3.3+dfsg-2build1_riscv64.deb'. pkgstripfiles: processing control file: debian/.debhelper/augustus/dbgsym-root/DEBIAN/control, package augustus-dbgsym, directory debian/.debhelper/augustus/dbgsym-root dpkg-deb: building package 'augustus-dbgsym' in 'debian/.debhelper/scratch-space/build-augustus/augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.deb'. Renaming augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.deb to augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../augustus_3.3.3+dfsg-2build1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-04-06T12:56:09Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ augustus_3.3.3+dfsg-2build1_riscv64.changes: -------------------------------------------- Format: 1.8 Date: Sun, 22 Mar 2020 16:34:00 +0100 Source: augustus Binary: augustus Architecture: riscv64 Version: 3.3.3+dfsg-2build1 Distribution: focal Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: augustus - gene prediction in eukaryotic genomes Changes: augustus (3.3.3+dfsg-2build1) focal; urgency=medium . * No-change rebuild for libgcc-s1 package name change. Checksums-Sha1: 2a3faaaef015eef7d9e01995141009fa5877aa24 11626764 augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.ddeb 62089232c80ada0012af7ed3491d30cd79e11930 8651 augustus_3.3.3+dfsg-2build1_riscv64.buildinfo 28070627775f745feb834fcb4e536f8a0b09a125 1111156 augustus_3.3.3+dfsg-2build1_riscv64.deb Checksums-Sha256: 9c68587b1f6529399846cd0628ccfb12ef96c7296b5e101f4da6a21b0e9115c8 11626764 augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.ddeb 80fd5a9b654a50f0c2aec5ee77f5b1275815aaf1e39612766cc374d69a39571c 8651 augustus_3.3.3+dfsg-2build1_riscv64.buildinfo a35acdbf15eb70c6648c49b195a795b68e34c4ac9de337d8ce5719d4b2203f25 1111156 augustus_3.3.3+dfsg-2build1_riscv64.deb Files: 07e4e7c54e3ba27a2abeba3eb183a992 11626764 debug optional augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.ddeb cca7d13a912ea557cbf70f1ac3227ac6 8651 science optional augustus_3.3.3+dfsg-2build1_riscv64.buildinfo 0320dd2f8b305b8e6da2eb56413c77d5 1111156 science optional augustus_3.3.3+dfsg-2build1_riscv64.deb /<>/augustus_3.3.3+dfsg-2build1_riscv64.changes.new could not be renamed to /<>/augustus_3.3.3+dfsg-2build1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: augustus Binary: augustus augustus-data augustus-doc Architecture: riscv64 Version: 3.3.3+dfsg-2build1 Checksums-Md5: 07e4e7c54e3ba27a2abeba3eb183a992 11626764 augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.ddeb 0320dd2f8b305b8e6da2eb56413c77d5 1111156 augustus_3.3.3+dfsg-2build1_riscv64.deb Checksums-Sha1: 2a3faaaef015eef7d9e01995141009fa5877aa24 11626764 augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.ddeb 28070627775f745feb834fcb4e536f8a0b09a125 1111156 augustus_3.3.3+dfsg-2build1_riscv64.deb Checksums-Sha256: 9c68587b1f6529399846cd0628ccfb12ef96c7296b5e101f4da6a21b0e9115c8 11626764 augustus-dbgsym_3.3.3+dfsg-2build1_riscv64.ddeb a35acdbf15eb70c6648c49b195a795b68e34c4ac9de337d8ce5719d4b2203f25 1111156 augustus_3.3.3+dfsg-2build1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Mon, 06 Apr 2020 12:55:59 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: asciidoctor (= 2.0.10-2), autoconf (= 2.69-11.1), automake (= 1:1.16.1-4ubuntu6), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu4), base-passwd (= 3.5.47), bash (= 5.0-6ubuntu1), binutils (= 2.34-5ubuntu1), binutils-common (= 2.34-5ubuntu1), binutils-riscv64-linux-gnu (= 2.34-5ubuntu1), bsdmainutils (= 11.1.2ubuntu3), bsdutils (= 1:2.34-0.1ubuntu8), build-essential (= 12.8ubuntu1), bzip2 (= 1.0.8-2), ca-certificates (= 20190110ubuntu1), coreutils (= 8.30-3ubuntu2), cpp (= 4:9.3.0-1ubuntu2), cpp-9 (= 9.3.0-10ubuntu1), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.10ubuntu1), debianutils (= 4.9.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.3-2), 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1.1.1d-2ubuntu6), libssl1.1 (= 1.1.1d-2ubuntu6), libstdc++-9-dev (= 9.3.0-10ubuntu1), libstdc++6 (= 10-20200324-1ubuntu1), libsub-override-perl (= 0.09-2), libsuitesparse-dev (= 1:5.7.1+dfsg-2), libsuitesparseconfig5 (= 1:5.7.1+dfsg-2), libsystemd0 (= 245.2-1ubuntu3), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2-0ubuntu2), libtool (= 2.4.6-13), libuchardet0 (= 0.0.6-3build1), libudev1 (= 245.2-1ubuntu3), libumfpack5 (= 1:5.7.1+dfsg-2), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1ubuntu8), libwind0-heimdal (= 7.7.0+dfsg-1ubuntu1), libxml2 (= 2.9.10+dfsg-4build1), libyaml-0-2 (= 0.2.2-1), libzstd1 (= 1.4.4+dfsg-3), linux-libc-dev (= 5.4.0-21.25), login (= 1:4.8.1-1ubuntu3), lsb-base (= 11.1.0ubuntu2), lzma-dev (= 9.22-2.1build1), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-0ubuntu2), ncurses-bin (= 6.2-0ubuntu2), openssl (= 1.1.1d-2ubuntu6), patch (= 2.7.6-6), perl (= 5.30.0-9build1), perl-base (= 5.30.0-9build1), perl-modules-5.30 (= 5.30.0-9build1), po-debconf (= 1.0.21), rake (= 13.0.1-2), readline-common (= 8.0-4), ruby (= 1:2.7), ruby-asciidoctor (= 2.0.10-2), ruby-did-you-mean (= 1.2.1-1), ruby-minitest (= 5.13.0-1), ruby-net-telnet (= 0.1.1-2), ruby-power-assert (= 1.1.7-1), ruby-test-unit (= 3.3.4-1), ruby-xmlrpc (= 0.3.0-2), ruby2.7 (= 2.7.0-4+riscv64.1), rubygems-integration (= 1.16), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-2.1ubuntu1), tar (= 1.30+dfsg-7), tzdata (= 2019c-3ubuntu1), util-linux (= 2.34-0.1ubuntu8), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1584891240" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ augustus_3.3.3+dfsg-2build1_riscv64.deb --------------------------------------- new Debian package, version 2.0. size 1111156 bytes: control archive=4704 bytes. 1334 bytes, 23 lines control 9804 bytes, 130 lines md5sums Package: augustus Version: 3.3.3+dfsg-2build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4034 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.27), libgcc-s1 (>= 4.5), libstdc++6 (>= 9), zlib1g (>= 1:1.2.3.3), augustus-data Built-Using: samtools-legacy (= 0.1.19-4) Section: science Priority: optional Homepage: http://bioinf.uni-greifswald.de/augustus/ Description: gene prediction in eukaryotic genomes AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes. drwxr-xr-x root/root 0 2020-03-22 15:34 ./ drwxr-xr-x root/root 0 2020-03-22 15:34 ./usr/ drwxr-xr-x root/root 0 2020-03-22 15:34 ./usr/bin/ -rwxr-xr-x root/root 14640 2020-03-22 15:34 ./usr/bin/aln2wig -rwxr-xr-x root/root 1103592 2020-03-22 15:34 ./usr/bin/augustus -rwxr-xr-x root/root 32224 2020-03-22 15:34 ./usr/bin/bam2hints -rwxr-xr-x root/root 86168 2020-03-22 15:34 ./usr/bin/bam2wig -rwxr-xr-x root/root 77944 2020-03-22 15:34 ./usr/bin/checkTargetSortedness -rwxr-xr-x root/root 14680 2020-03-22 15:34 ./usr/bin/compileSpliceCands -rwxr-xr-x root/root 1256688 2020-03-22 15:34 ./usr/bin/etraining -rwxr-xr-x root/root 229088 2020-03-22 15:34 ./usr/bin/fastBlockSearch -rwxr-xr-x root/root 171232 2020-03-22 15:34 ./usr/bin/filterBam -rwxr-xr-x root/root 106096 2020-03-22 15:34 ./usr/bin/homGeneMapping -rwxr-xr-x root/root 117720 2020-03-22 15:34 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2020-03-22 15:34 ./usr/share/man/man1/prepareAlign.1.gz -rw-r--r-- root/root 1380 2020-03-22 15:34 ./usr/share/man/man1/utrrnaseq.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 1087576 Build-Time: 2491 Distribution: focal Host Architecture: riscv64 Install-Time: 418 Job: augustus_3.3.3+dfsg-2build1.dsc Machine Architecture: riscv64 Package: augustus Package-Time: 3038 Source-Version: 3.3.3+dfsg-2build1 Space: 1087576 Status: successful Version: 3.3.3+dfsg-2build1 -------------------------------------------------------------------------------- Finished at 2020-04-06T12:56:09Z Build needed 00:50:38, 1087576k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100189 Scanning for processes to kill in build PACKAGEBUILD-19100189 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100189 Stopping target for build PACKAGEBUILD-19100189 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100189 Removing build PACKAGEBUILD-19100189