https://launchpad.net/ubuntu/+archive/test-rebuild-20220617-kinetic/+build/24062841 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-023 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_215~563~ubuntu20.04.1 python3-lpbuildd_215~563~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 23 Jun 13:52:52 ntpdate[1871]: adjust time server 10.211.37.1 offset -0.000421 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24062841 --image-type chroot /home/buildd/filecache-default/4d18961cd05542d5def75b14497015b674c37821 Creating target for build PACKAGEBUILD-24062841 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24062841 Starting target for build PACKAGEBUILD-24062841 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24062841 'deb http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic main' 'deb http://ftpmaster.internal/ubuntu kinetic main universe' Overriding sources.list in build-PACKAGEBUILD-24062841 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24062841 Adding trusted keys to build-PACKAGEBUILD-24062841 pub rsa1024/1E9377A2BA9EF27F 2009-10-22 [SC] Key fingerprint = 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid Launchpad Toolchain builds RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24062841 Updating target for build PACKAGEBUILD-24062841 Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic InRelease [23.8 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:3 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 Packages [9632 B] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main Translation-en [4132 B] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 Packages [1398 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5730 kB] Fetched 22.2 MB in 5s (4715 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libgprofng0 util-linux-extra The following packages will be upgraded: adduser apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils cpp-11 dash dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gcc-12-base init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libitm1 libkeyutils1 liblsan0 liblzma5 libmount1 libncurses6 libncursesw6 libpng16-16 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd pinentry-curses policyrcd-script-zg2 readline-common systemd systemd-sysv util-linux xz-utils 84 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 79.8 MB of archives. After this operation, 5300 kB of additional disk space will be used. Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf0 amd64 2.38.50.20220615-4ubuntu1 [103 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-files amd64 12.2ubuntu1 [62.6 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf-nobfd0 amd64 2.38.50.20220615-4ubuntu1 [107 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:6 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-x86-64-linux-gnu amd64 2.38.50.20220615-4ubuntu1 [2476 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libatomic1 amd64 12.1.0-2ubuntu1 [10.4 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libubsan1 amd64 12.1.0-2ubuntu1 [969 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libquadmath0 amd64 12.1.0-2ubuntu1 [152 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblsan0 amd64 12.1.0-2ubuntu1 [1060 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 libitm1 amd64 12.1.0-2ubuntu1 [29.5 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgomp1 amd64 12.1.0-2ubuntu1 [125 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-12-base amd64 12.1.0-2ubuntu1 [18.8 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-s1 amd64 12.1.0-2ubuntu1 [54.2 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcc1-0 amd64 12.1.0-2ubuntu1 [46.6 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++6 amd64 12.1.0-2ubuntu1 [679 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcrypt20 amd64 1.10.1-2ubuntu1 [524 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma5 amd64 5.2.5-2.1 [99.2 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd-sysv amd64 249.11-0ubuntu4 [10.2 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapparmor1 amd64 3.0.4-2ubuntu3 [38.0 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgnutls30 amd64 3.7.6-2ubuntu1 [968 kB] Get:23 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libbinutils amd64 2.38.50.20220615-4ubuntu1 [655 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main amd64 libip4tc2 amd64 1.8.7-1ubuntu6 [19.7 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main amd64 libblkid1 amd64 2.38-4ubuntu1 [103 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main amd64 libselinux1 amd64 3.4-1 [77.6 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmount1 amd64 2.38-4ubuntu1 [121 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsmartcols1 amd64 2.38-4ubuntu1 [50.8 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 login amd64 1:4.11.1+dfsg1-2ubuntu1 [183 kB] Get:30 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils amd64 2.38.50.20220615-4ubuntu1 [3292 B] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux-extra amd64 2.38-4ubuntu1 [83.8 kB] Get:32 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-common amd64 2.38.50.20220615-4ubuntu1 [224 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux amd64 2.38-4ubuntu1 [1069 kB] Get:34 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libgprofng0 amd64 2.38.50.20220615-4ubuntu1 [963 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 mount amd64 2.38-4ubuntu1 [114 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage-common all 3.4-1 [9828 B] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsepol2 amd64 3.4-2 [294 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage2 amd64 3.4-1 [91.8 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 passwd amd64 1:4.11.1+dfsg1-2ubuntu1 [765 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 adduser all 3.121ubuntu1 [150 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd amd64 249.11-0ubuntu4 [4517 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsystemd0 amd64 249.11-0ubuntu4 [314 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 libudev1 amd64 249.11-0ubuntu4 [76.1 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapt-pkg6.0 amd64 2.5.0 [896 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg amd64 1.21.8ubuntu1 [1333 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-8ubuntu1 [88.2 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 init-system-helpers all 1.63 [38.7 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 apt amd64 2.5.0 [1370 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 logsave amd64 1.46.5-2ubuntu2 [9914 B] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 libext2fs2 amd64 1.46.5-2ubuntu2 [205 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 e2fsprogs amd64 1.46.5-2ubuntu2 [585 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 init amd64 1.63 [5674 B] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcap-ng0 amd64 0.7.9-4 [12.1 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.9 [717 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtinfo6 amd64 6.3+20220423-2 [99.6 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main amd64 libuuid1 amd64 2.38-4ubuntu1 [23.2 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcom-err2 amd64 1.46.5-2ubuntu2 [9074 B] Get:62 http://ftpmaster.internal/ubuntu kinetic/main amd64 libss2 amd64 1.46.5-2ubuntu2 [12.3 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main amd64 mawk amd64 1.3.4.20200120-3.1 [109 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic/main amd64 libkeyutils1 amd64 1.6.1-3ubuntu1 [10.1 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic/main amd64 readline-common all 8.1.2-1.2 [53.6 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main amd64 libreadline8 amd64 8.1.2-1.2 [153 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsqlite3-0 amd64 3.38.5-1 [646 kB] 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http://ftpmaster.internal/ubuntu kinetic/main amd64 cpp-11 amd64 11.3.0-3ubuntu1 [9910 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11-base amd64 11.3.0-3ubuntu1 [20.8 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg-dev all 1.21.8ubuntu1 [1069 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdpkg-perl all 1.21.8ubuntu1 [237 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main amd64 lto-disabled-list all 27 [12.4 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfakeroot amd64 1.29-1ubuntu1 [31.1 kB] Get:84 http://ftpmaster.internal/ubuntu kinetic/main amd64 fakeroot amd64 1.29-1ubuntu1 [60.0 kB] Get:85 http://ftpmaster.internal/ubuntu kinetic/main amd64 pinentry-curses amd64 1.2.0-1ubuntu1 [34.5 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic/main amd64 policyrcd-script-zg2 all 0.1-3.1 [5730 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.8 MB in 4s (18.3 MB/s) 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Setting up libstdc++-11-dev:amd64 (11.3.0-3ubuntu1) ... Setting up gcc-11 (11.3.0-3ubuntu1) ... Setting up g++-11 (11.3.0-3ubuntu1) ... Processing triggers for debianutils (5.7-0.2) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24062841 amd64 kinetic -c chroot:build-PACKAGEBUILD-24062841 --arch=amd64 --dist=kinetic --nolog -A reapr_1.0.18+dfsg-5build1.dsc Initiating build PACKAGEBUILD-24062841 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lgw01-amd64-023.buildd +==============================================================================+ | reapr 1.0.18+dfsg-5build1 (amd64) Thu, 23 Jun 2022 13:53:33 +0000 | +==============================================================================+ Package: reapr Version: 1.0.18+dfsg-5build1 Source Version: 1.0.18+dfsg-5build1 Distribution: kinetic Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24062841/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/reapr-vQS7BJ/resolver-7mJ6zB' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- reapr_1.0.18+dfsg-5build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/reapr-vQS7BJ/reapr-1.0.18+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/reapr-vQS7BJ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl, 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 [453 B] Get:5 copy:/<>/apt_archive ./ Packages [537 B] Fetched 1947 B in 0s (71.2 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbambamc0 libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libhtscodecs2 libice6 libicu71 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp25 liblapack3 libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libmd0 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 librtmp1 libruby3.0 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db po-debconf r-base r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration samtools smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html ri ruby-dev bundler cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-base-html r-doc-html r-base-dev fonts-lato libjs-jquery libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbambamc0 libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libhtscodecs2 libice6 libicu71 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp25 liblapack3 libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libmd0 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 librtmp1 libruby3.0 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db po-debconf r-base r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration samtools sbuild-build-depends-main-dummy smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 145 newly installed, 0 to remove and 0 not upgraded. Need to get 96.8 MB of archives. After this operation, 233 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [758 B] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmd0 amd64 1.0.4-1build1 [23.0 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 libbsd0 amd64 0.11.6-1 [44.5 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 libelf1 amd64 0.187-1 [51.3 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 libexpat1 amd64 2.4.8-1 [90.6 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfribidi0 amd64 1.0.8-2ubuntu3.1 [26.1 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libglib2.0-0 amd64 2.72.2-2 [1435 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libicu71 amd64 71.1-3 [10.6 MB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxml2 amd64 2.9.14+dfsg-1 [756 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 libyaml-0-2 amd64 0.2.2-1build2 [51.6 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 ucf all 3.0043 [56.1 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdextrautils amd64 2.38-4ubuntu1 [71.1 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmagic-mgc amd64 1:5.41-4 [257 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmagic1 amd64 1:5.41-4 [87.3 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 file amd64 1:5.41-4 [21.5 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 gettext-base amd64 0.21-6 [37.9 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main amd64 groff-base amd64 1.22.4-8build1 [955 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main amd64 libedit2 amd64 3.1-20210910-1build1 [96.8 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnghttp2-14 amd64 1.47.0-1 [69.0 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpipeline1 amd64 1.5.6-1 [23.1 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpsl5 amd64 0.21.0-1.2build2 [58.4 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:24 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxcb1 amd64 1.14-3ubuntu3 [49.0 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main amd64 libx11-data all 2:1.7.5-1 [119 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libx11-6 amd64 2:1.7.5-1 [666 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxext6 amd64 2:1.3.4-1build1 [31.8 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 man-db amd64 2.10.2-1 [1187 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 rubygems-integration all 1.18 [5336 B] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 rake all 13.0.6-3 [61.6 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby-net-telnet all 0.1.1-2.1 [13.1 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby-webrick all 1.7.0-3 [51.8 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby-xmlrpc all 0.3.2-2 [24.8 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 libruby3.0 amd64 3.0.2-7ubuntu2 [5115 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby3.0 amd64 3.0.2-7ubuntu2 [50.1 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby-rubygems all 3.3.15-1 [231 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby amd64 1:3.0~exp1 [5100 B] Get:39 http://ftpmaster.internal/ubuntu kinetic/universe amd64 ruby-asciidoctor all 2.0.16-2 [173 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/universe amd64 asciidoctor all 2.0.16-2 [44.3 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsigsegv2 amd64 2.13-1ubuntu3 [14.6 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 m4 amd64 1.4.18-5ubuntu2 [199 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 autoconf all 2.71-2 [338 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 autopoint all 0.21-6 [421 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-10build1 [156 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjsoncpp25 amd64 1.9.5-4 [80.3 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/universe amd64 bamtools amd64 2.5.1+dfsg-10build1 [164 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdebhelper-perl all 13.7.1ubuntu1 [66.9 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtool all 2.4.7-4 [166 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 dh-autoreconf all 20 [16.1 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsub-override-perl all 0.09-3 [9756 B] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdw1 amd64 0.187-1 [247 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main amd64 debugedit amd64 1:5.0-4build1 [47.2 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main amd64 dwz amd64 0.14-1build2 [105 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main amd64 gettext amd64 0.21-6 [862 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main amd64 debhelper all 13.7.1ubuntu1 [940 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic/main amd64 libbrotli1 amd64 1.0.9-2build6 [315 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfreetype6 amd64 2.12.1+dfsg-3 [387 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main amd64 fonts-dejavu-core all 2.37-2build1 [1041 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic/main amd64 fontconfig-config all 2.13.1-4.4ubuntu1 [28.2 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfontconfig1 amd64 2.13.1-4.4ubuntu1 [129 kB] Get:69 http://ftpmaster.internal/ubuntu kinetic/main amd64 fontconfig amd64 2.13.1-4.4ubuntu1 [176 kB] Get:70 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libbambamc0 amd64 0.0.50-6 [39.4 kB] Get:71 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libbamtools-dev amd64 2.5.1+dfsg-10build1 [226 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic/main amd64 libblas3 amd64 3.10.1-2 [228 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpixman-1-0 amd64 0.40.0-1build4 [264 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxcb-render0 amd64 1.14-3ubuntu3 [16.4 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxcb-shm0 amd64 1.14-3ubuntu3 [5780 B] Get:76 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcairo2 amd64 1.16.0-5ubuntu2 [628 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-6ubuntu1 [20.5 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsasl2-2 amd64 2.1.28+dfsg-6ubuntu1 [55.9 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main amd64 libldap-2.5-0 amd64 2.5.12+dfsg-2ubuntu1 [180 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main amd64 libssh-4 amd64 0.9.6-2build1 [184 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcurl3-gnutls amd64 7.83.1-2 [280 kB] Get:84 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcurl4 amd64 7.83.1-2 [285 kB] Get:85 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcurl4-gnutls-dev amd64 7.83.1-2 [381 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdatrie1 amd64 0.2.13-2 [19.9 kB] Get:87 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdeflate0 amd64 1.10-2 [70.9 kB] Get:88 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdeflate-dev amd64 1.10-2 [59.2 kB] Get:89 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libfile-copy-link-perl all 0.140-3 [15.5 kB] Get:90 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgfortran5 amd64 12.1.0-2ubuntu1 [875 kB] Get:91 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgraphite2-3 amd64 1.3.14-1build2 [71.3 kB] Get:92 http://ftpmaster.internal/ubuntu kinetic/main amd64 libharfbuzz0b amd64 2.7.4-1ubuntu4 [352 kB] Get:93 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhtscodecs2 amd64 1.2.1-1 [57.0 kB] Get:94 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhts3 amd64 1.13+ds-2build2 [388 kB] Get:95 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma-dev amd64 5.2.5-2.1 [157 kB] Get:96 http://ftpmaster.internal/ubuntu kinetic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu9 [164 kB] Get:97 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhts-dev amd64 1.13+ds-2build2 [5561 kB] Get:98 http://ftpmaster.internal/ubuntu kinetic/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:99 http://ftpmaster.internal/ubuntu kinetic/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] Get:100 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg-turbo8 amd64 2.1.2-0ubuntu1 [134 kB] Get:101 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg8 amd64 8c-2ubuntu10 [2264 B] Get:102 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblapack3 amd64 3.10.1-2 [2492 kB] Get:103 http://ftpmaster.internal/ubuntu kinetic/main amd64 libthai-data all 0.1.29-1build1 [162 kB] Get:104 http://ftpmaster.internal/ubuntu kinetic/main amd64 libthai0 amd64 0.1.29-1build1 [19.2 kB] Get:105 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpango-1.0-0 amd64 1.50.7+ds-1 [224 kB] Get:106 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpangoft2-1.0-0 amd64 1.50.7+ds-1 [52.0 kB] Get:107 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpangocairo-1.0-0 amd64 1.50.7+ds-1 [38.2 kB] Get:108 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpaper1 amd64 1.1.28build2 [13.8 kB] Get:109 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpaper-utils amd64 1.1.28build2 [8674 B] Get:110 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] Get:111 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libtabixpp0 amd64 1.1.0-6 [9998 B] Get:112 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libtabixpp-dev amd64 1.1.0-6 [7632 B] Get:113 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtcl8.6 amd64 8.6.12+dfsg-1build1 [990 kB] Get:114 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjbig0 amd64 2.1-3.1build3 [28.9 kB] Get:115 http://ftpmaster.internal/ubuntu kinetic/main amd64 libwebp7 amd64 1.2.2-2 [206 kB] Get:116 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtiff5 amd64 4.4.0~rc1-1 [183 kB] Get:117 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxft2 amd64 2.3.4-1 [41.8 kB] Get:118 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] Get:119 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtk8.6 amd64 8.6.12-1build1 [784 kB] Get:120 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxt6 amd64 1:1.2.1-1 [177 kB] Get:121 http://ftpmaster.internal/ubuntu kinetic/main amd64 zip amd64 3.0-12build2 [176 kB] Get:122 http://ftpmaster.internal/ubuntu kinetic/main amd64 unzip amd64 6.0-26ubuntu3 [174 kB] Get:123 http://ftpmaster.internal/ubuntu kinetic/main amd64 xdg-utils all 1.1.3-4.1ubuntu2 [62.0 kB] Get:124 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-base-core amd64 4.2.0-1ubuntu1 [28.3 MB] Get:125 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-boot all 1.3-28-2 [618 kB] Get:126 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-cluster amd64 2.1.3-1 [543 kB] Get:127 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-foreign amd64 0.8.82-1 [244 kB] Get:128 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-mass amd64 7.3-57-1 [1115 kB] Get:129 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-kernsmooth amd64 2.23-20-1 [90.3 kB] Get:130 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-lattice amd64 0.20-45-3 [1130 kB] Get:131 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-nlme amd64 3.1.158-1 [2210 kB] Get:132 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-matrix amd64 1.4-1-1 [4329 kB] Get:133 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-mgcv amd64 1.8-40-1 [2979 kB] Get:134 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-survival amd64 3.3-1-1 [6588 kB] Get:135 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-rpart amd64 4.1.16-1 [892 kB] Get:136 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-class amd64 7.3-20-1 [87.9 kB] Get:137 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-nnet amd64 7.3-17-1 [112 kB] Get:138 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-spatial amd64 7.3-15-1 [132 kB] Get:139 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-cran-codetools all 0.2-18-1 [90.8 kB] Get:140 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-recommended all 4.2.0-1ubuntu1 [2622 B] Get:141 http://ftpmaster.internal/ubuntu kinetic/universe amd64 r-base all 4.2.0-1ubuntu1 [9288 B] Get:142 http://ftpmaster.internal/ubuntu kinetic/universe amd64 samtools amd64 1.13-4 [520 kB] Get:143 http://ftpmaster.internal/ubuntu kinetic/universe amd64 smalt amd64 0.7.6-12 [101 kB] Get:144 http://ftpmaster.internal/ubuntu kinetic/universe amd64 snpomatic amd64 1.0-5 [83.4 kB] Get:145 http://ftpmaster.internal/ubuntu kinetic/universe amd64 tabix amd64 1.13+ds-2build2 [349 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 96.8 MB in 5s (18.1 MB/s) Selecting previously unselected package libmd0:amd64. (Reading database ... 13496 files and directories currently installed.) Preparing to unpack .../000-libmd0_1.0.4-1build1_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-1build1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../001-libbsd0_0.11.6-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.6-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../002-libelf1_0.187-1_amd64.deb ... Unpacking libelf1:amd64 (0.187-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../003-libexpat1_2.4.8-1_amd64.deb ... Unpacking libexpat1:amd64 (2.4.8-1) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../004-libfribidi0_1.0.8-2ubuntu3.1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.8-2ubuntu3.1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../005-libglib2.0-0_2.72.2-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.72.2-2) ... 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Setting up libicu71:amd64 (71.1-3) ... Setting up libxau6:amd64 (1:1.0.9-1build5) ... Setting up libpsl5:amd64 (0.21.0-1.2build2) ... Setting up libfile-copy-link-perl (0.140-3) ... Setting up bsdextrautils (2.38-4ubuntu1) ... Setting up libdatrie1:amd64 (0.2.13-2) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.2-1build2) ... Setting up libglib2.0-0:amd64 (2.72.2-2) ... No schema files found: doing nothing. Setting up unzip (6.0-26ubuntu3) ... Setting up libdebhelper-perl (13.7.1ubuntu1) ... Setting up libbrotli1:amd64 (1.0.9-2build6) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.47.0-1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up libdeflate0:amd64 (1.10-2) ... Setting up gettext-base (0.21-6) ... Setting up rubygems-integration (1.18) ... Setting up file (1:5.41-4) ... Setting up libjbig0:amd64 (2.1-3.1build3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-6ubuntu1) ... Setting up zip (3.0-12build2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libfreetype6:amd64 (2.12.1+dfsg-3) ... Setting up libx11-data (2:1.7.5-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up ruby-net-telnet (0.1.1-2.1) ... Setting up libsigsegv2:amd64 (2.13-1ubuntu3) ... Setting up libfribidi0:amd64 (1.0.8-2ubuntu3.1) ... Setting up libbambamc0:amd64 (0.0.50-6) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-10build1) ... Setting up libtcl8.6:amd64 (8.6.12+dfsg-1build1) ... Setting up autopoint (0.21-6) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up fonts-dejavu-core (2.37-2build1) ... Setting up ucf (3.0043) ... Setting up libjpeg-turbo8:amd64 (2.1.2-0ubuntu1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-6ubuntu1) ... Setting up libssh-4:amd64 (0.9.6-2build1) ... Setting up libgfortran5:amd64 (12.1.0-2ubuntu1) ... Setting up libwebp7:amd64 (1.2.2-2) ... Setting up ruby-webrick (1.7.0-3) ... Setting up liblzma-dev:amd64 (5.2.5-2.1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9) ... Setting up libmd0:amd64 (1.0.4-1build1) ... Setting up bamtools (2.5.1+dfsg-10build1) ... Setting up snpomatic (1.0-5) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-3) ... Setting up libharfbuzz0b:amd64 (2.7.4-1ubuntu4) ... Setting up libthai-data (0.1.29-1build1) ... Setting up libbsd0:amd64 (0.11.6-1) ... Setting up libdeflate-dev:amd64 (1.10-2) ... Setting up tabix (1.13+ds-2build2) ... Setting up libelf1:amd64 (0.187-1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1) ... Setting up xdg-utils (1.1.3-4.1ubuntu2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libjpeg8:amd64 (8c-2ubuntu10) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up smalt (0.7.6-12) ... Setting up libpaper1:amd64 (1.1.28build2) ... Creating config file /etc/papersize with new version Setting up libice6:amd64 (2:1.0.10-1build2) ... Setting up libdw1:amd64 (0.187-1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:amd64 (3.10.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3ubuntu3) ... Setting up gettext (0.21-6) ... Setting up libtool (2.4.7-4) ... Setting up libxcb-render0:amd64 (1.14-3ubuntu3) ... Setting up fontconfig-config (2.13.1-4.4ubuntu1) ... Setting up libedit2:amd64 (3.1-20210910-1build1) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up libxcb-shm0:amd64 (1.14-3ubuntu3) ... Setting up libpaper-utils (1.1.28build2) ... Setting up libldap-2.5-0:amd64 (2.5.12+dfsg-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:amd64 (0.1.29-1build1) ... Setting up libbamtools-dev:amd64 (2.5.1+dfsg-10build1) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libcurl4:amd64 (7.83.1-2) ... Setting up libx11-6:amd64 (2:1.7.5-1) ... Setting up libtiff5:amd64 (4.4.0~rc1-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.4ubuntu1) ... Setting up libsm6:amd64 (2:1.2.3-1build2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up fontconfig (2.13.1-4.4ubuntu1) ... Regenerating fonts cache... done. Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.50.7+ds-1) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up libcurl3-gnutls:amd64 (7.83.1-2) ... Setting up libcurl4-gnutls-dev:amd64 (7.83.1-2) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:amd64 (1.16.0-5ubuntu2) ... Setting up dh-autoreconf (20) ... Setting up libxt6:amd64 (1:1.2.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1build2) ... Setting up libpangoft2-1.0-0:amd64 (1.50.7+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.7+ds-1) ... Setting up libxft2:amd64 (2.3.4-1) ... Setting up libhts3:amd64 (1.13+ds-2build2) ... Setting up libtk8.6:amd64 (8.6.12-1build1) ... Setting up libhts-dev:amd64 (1.13+ds-2build2) ... Setting up debhelper (13.7.1ubuntu1) ... Setting up samtools (1.13-4) ... Setting up r-base-core (4.2.0-1ubuntu1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-lattice (0.20-45-3) ... Setting up r-cran-nlme (3.1.158-1) ... Setting up r-cran-cluster (2.1.3-1) ... Setting up libtabixpp0:amd64 (1.1.0-6) ... Setting up r-cran-nnet (7.3-17-1) ... Setting up r-cran-codetools (0.2-18-1) ... Setting up r-cran-boot (1.3-28-2) ... Setting up r-cran-spatial (7.3-15-1) ... Setting up r-cran-mass (7.3-57-1) ... Setting up r-cran-foreign (0.8.82-1) ... Setting up r-cran-matrix (1.4-1-1) ... Setting up r-cran-kernsmooth (2.23-20-1) ... Setting up r-cran-mgcv (1.8-40-1) ... Setting up libtabixpp-dev:amd64 (1.1.0-6) ... Setting up r-cran-class (7.3-20-1) ... Setting up r-cran-survival (3.3-1-1) ... Setting up r-cran-rpart (4.1.16-1) ... Setting up r-recommended (4.2.0-1ubuntu1) ... Setting up r-base (4.2.0-1ubuntu1) ... Setting up ruby-rubygems (3.3.15-1) ... Setting up ruby (1:3.0~exp1) ... Setting up ruby-asciidoctor (2.0.16-2) ... Setting up rake (13.0.6-3) ... Setting up asciidoctor (2.0.16-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libruby3.0:amd64 (3.0.2-7ubuntu2) ... Setting up ruby3.0 (3.0.2-7ubuntu2) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.38.50.20220615-4ubuntu1 dpkg-dev_1.21.8ubuntu1 g++-11_11.3.0-3ubuntu1 gcc-11_11.3.0-3ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-3ubuntu1 libstdc++6_12.1.0-2ubuntu1 linux-libc-dev_5.15.0-27.28 Package versions: adduser_3.121ubuntu1 advancecomp_2.1-2.1ubuntu2 apt_2.5.0 asciidoctor_2.0.16-2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 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r-cran-mgcv_1.8-40-1 r-cran-nlme_3.1.158-1 r-cran-nnet_7.3-17-1 r-cran-rpart_4.1.16-1 r-cran-spatial_7.3-15-1 r-cran-survival_3.3-1-1 r-recommended_4.2.0-1ubuntu1 rake_13.0.6-3 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 ruby_1:3.0~exp1 ruby-asciidoctor_2.0.16-2 ruby-net-telnet_0.1.1-2.1 ruby-rubygems_3.3.15-1 ruby-webrick_1.7.0-3 ruby-xmlrpc_0.3.2-2 ruby3.0_3.0.2-7ubuntu2 rubygems-integration_1.18 samtools_1.13-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 smalt_0.7.6-12 snpomatic_1.0-5 systemd_249.11-0ubuntu4 systemd-sysv_249.11-0ubuntu4 sysvinit-utils_3.01-1ubuntu1 tabix_1.13+ds-2build2 tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043 unzip_6.0-26ubuntu3 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 x11-common_1:7.7+23ubuntu2 xdg-utils_1.1.3-4.1ubuntu2 xz-utils_5.2.5-2.1 zip_3.0-12build2 zlib1g_1:1.2.11.dfsg-2ubuntu9 zlib1g-dev_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: reapr Binary: reapr Architecture: any Version: 1.0.18+dfsg-5build1 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://www.sanger.ac.uk/science/tools/reapr Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/reapr Vcs-Git: https://salsa.debian.org/med-team/reapr.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 12), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl Package-List: reapr deb science optional arch=any Checksums-Sha1: 3534f93653fc8eb621226e51ef212835b1281af9 74636 reapr_1.0.18+dfsg.orig.tar.gz 06363b3fa65c7ba0e01f9718fd8deca6ba12142d 319688 reapr_1.0.18+dfsg-5build1.debian.tar.xz Checksums-Sha256: 70a9c252474fbbd36360c49589af18ca1599289eff2e98fb8cb7614583cb28a6 74636 reapr_1.0.18+dfsg.orig.tar.gz 5560783e95697294b8f8e8ca379c23902378ee993fc3355b1e8b89a784c07f0e 319688 reapr_1.0.18+dfsg-5build1.debian.tar.xz Files: 061dfbfe97a0bdffe3a4b9e4be8142d3 74636 reapr_1.0.18+dfsg.orig.tar.gz b72eb045d31623da69504b0694acd2fb 319688 reapr_1.0.18+dfsg-5build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJEBAEBCAAuFiEE1WVxuIqLuvFAv2PWvX6qYHePpvUFAl56GMwQHGRva29AdWJ1 bnR1LmNvbQAKCRC9fqpgd4+m9ZSKD/0anQd5UxEPrxEbESYA91P72edLotBVO3qq flN8/xUEGTp2gZu/tiqIxoOC8rHeyuRVrm/l9j7jDY6tG5LsYLxeNXX1Cx0VMKUE /xzTbusceUrZaLbWXSAXz6Dsw8vetAdm6TbQFBxxVO4v2RIbwg0ZAX6Hq4125Aou ikFjPB9LZYQaDaGeiPATKoEEFGZTyZImznzg5r+YvC72CMQWD/e/sp1Ejs2IhRI7 OlhlfbUV5x3DsQb2UpVyPrJ6TB5Jo5DjcpFPYDSTnBmyNVKuaMNJ4G9NQ9RZEVVd ApSfKbmssHTrRwCVkrzHQk50i6iiyaNNm3zMO+xEIHk0kExKIQzfiQD5u4tvOrhU 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info: applying fix_sort_samtools13 dpkg-source: info: applying ld_as_needed Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-24062841 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24062841 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24062841 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 reapr dpkg-buildpackage: info: source version 1.0.18+dfsg-5build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf /<>/debian/man_src/*.html /<>/debian/man_src/*.? rm -rf /<>/debian/man rm -rf /<>/debian/test dh_auto_clean -- make[1]: Leaving directory '/<>' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/<>' cd src && /usr/bin/make make[2]: Entering directory '/<>/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c errorWindow.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c histogram.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_score.cpp task_score.cpp: In function ‘int main(int, char**)’: task_score.cpp:235:79: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 235 | map > >::iterator p = globalGaps.find(currentRefID); | ^ g++ -o task_score -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_score.o errorWindow.o utils.o histogram.o -lbamtools -ltabixpp -lhts -lz -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c trianglePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c coveragePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_stats.cpp task_stats.cpp: In function ‘main’: task_stats.cpp:441:16: warning: ‘ti_perfect’ may be used uninitialized in this function [-Wmaybe-uninitialized] 441 | delete ti_perfect; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_stats.o trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_stats -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_break.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_break.o -lbamtools fasta.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_break -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fragCov.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fragCov.o -lbamtools coveragePlot.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2fragCov -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2insert.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2insert.o -lbamtools histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2insert -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fcdEstimate.cpp bam2fcdEstimate.cpp: In function ‘int main(int, char**)’: bam2fcdEstimate.cpp:84:34: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 84 | while (bamAlign.Position > triplot.centreCoord()) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bam2fcdEstimate.cpp: In function ‘void initialiseFCDHists(std::vector&, CmdLineOptions&)’: bam2fcdEstimate.cpp:210:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 210 | for (unsigned long i = 0; i <= ops.maxInsert; i++) | ~~^~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fcdEstimate.o -lbamtools histogram.o utils.o trianglePlot.o -ltabixpp -lhts -lz -o bam2fcdEstimate -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c make_plots.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include make_plots.o -o make_plots -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gaps.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gaps.o fasta.o -o fa2gaps -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gc.o fasta.o -o fa2gc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c scaff2contig.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include scaff2contig.o fasta.o -o scaff2contig -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c n50.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include n50.o fasta.o -o n50 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_gapresize.cpp task_gapresize.cpp: In function ‘int main(int, char**)’: task_gapresize.cpp:129:127: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~~~~~~~~~^~~~~~~~~ task_gapresize.cpp:129:148: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_gapresize.o -lbamtools utils.o trianglePlot.o fasta.o -ltabixpp -lhts -lz -o task_gapresize -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_fcdrate.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_fcdrate.o -ltabixpp -lhts -lz histogram.o utils.o -lbamtools -o task_fcdrate -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2perfect.cpp bam2perfect.cpp: In function ‘void writeAlignments(std::multimap&, BamTools::BamWriter&, long unsigned int)’: bam2perfect.cpp:213:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 213 | if (p->second.Position >= endPos) break; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2perfect.o -lbamtools utils.o -lbamtools -ltabixpp -lhts -lz -o bam2perfect -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' mkdir /<>/debian/test ln -s /<>/src/reapr.pl /<>/debian/test/reapr PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/<>/src:/<>/debian/test /<>/debian/tests/test-example [wgsim] seed = 42 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 1 sequences, total length: 1000111 foo 1384 T K + foo 4961 T W + foo 5885 - T - foo 9598 A C - foo 10177 G R + foo 11305 G K + foo 11592 G R + foo 13931 T - - foo 15907 C A - foo 17264 G K + foo 17780 A - - foo 18711 A W + foo 19249 T W + foo 19522 C S + foo 23053 T K + foo 23681 A R + foo 23730 C S + foo 24075 G S + foo 24555 G C - foo 26775 G K + foo 26896 C M + foo 27253 G K + foo 28210 T Y + foo 28224 A W + foo 28377 - G + foo 29035 G K + foo 29898 C M + foo 30274 A R + foo 30542 G K + foo 31566 A C - foo 32252 - A - foo 33303 T K + foo 33390 - G + foo 34073 A R + foo 34171 G R + foo 34718 T Y + foo 34801 - C + foo 35204 T W + foo 35342 G S + foo 35489 G T - foo 36153 A M + foo 36273 C S + foo 37356 G T - foo 37596 C S + foo 39308 T - - foo 40333 C G - foo 42295 T K + foo 42372 T Y + foo 44433 C G - foo 44630 - AG + foo 44902 T C - foo 47156 C A - foo 48210 C M + foo 48390 A R + foo 49652 C M + foo 52739 T Y + foo 52858 A M + foo 54737 A G - foo 55306 C T - foo 55434 C T - foo 59204 A W + foo 59300 G C - foo 59335 T Y + foo 59444 T - - foo 59531 C S + foo 59766 C Y + foo 61950 C S + foo 62887 G S + foo 63390 A G - foo 64365 G K + foo 64703 C S + foo 64932 C Y + foo 68383 - CG + foo 68464 A W + foo 68727 A W + foo 69080 A M + foo 72071 T C - foo 72720 - G - foo 73354 C T - foo 73637 G T - foo 74741 A M + foo 75101 C T - foo 75207 T K + foo 76400 T Y + foo 76780 A C - foo 77172 A W + foo 78385 C Y + foo 80705 C M + foo 82440 A R + foo 83021 G K + foo 83116 A - - foo 83846 T K + foo 84633 G S + foo 85891 G S + foo 87759 A C - foo 87778 T W + foo 88581 T K + foo 88606 T Y + foo 88880 A G - foo 89945 G C - foo 90728 T K + foo 91798 G R + foo 95957 G C - foo 96173 T W + foo 96665 A M + foo 98019 - G + foo 98131 A M + foo 98669 A R + foo 98719 G T - foo 99062 A W + foo 99590 A T - foo 100532 - TC + foo 103015 A W + foo 103172 G S + foo 103609 G R + foo 106549 T Y + foo 108808 C Y + foo 109191 G C - foo 111686 C G - foo 113436 C A - foo 113763 A W + foo 115671 C T - foo 117460 - A - foo 118193 G - - foo 118585 T K + foo 121219 A M + foo 121876 T K + foo 122071 T A - foo 124918 C G - foo 125300 G S + foo 125967 C S + foo 127443 G S + foo 127565 C Y + foo 128700 C A - foo 129912 G A - foo 130847 T W + foo 131677 G S + foo 132189 T C - foo 135878 CGGC - - foo 136825 T K + foo 138881 TGT - - foo 139288 A W + foo 141054 A W + foo 141055 - T + foo 141101 C S + foo 141404 A R + foo 142698 T C - foo 143990 C A - foo 144167 T Y + foo 144814 C Y + foo 146381 T Y + foo 146393 C A - foo 146510 A C - foo 147182 A W + foo 148783 T C - foo 149068 G S + foo 150208 T K + foo 151554 T W + foo 151709 C G - foo 153072 G R + foo 153307 T Y + foo 154050 G S + foo 154415 C S + foo 154594 G R + foo 155839 G T - foo 156106 G A - foo 159356 T W + foo 159926 A W + foo 160303 T K + foo 161323 C Y + foo 161904 G S + foo 162533 - ACC - foo 164738 C G - foo 165413 A R + foo 166944 C M + foo 167464 T Y + foo 168420 T C - foo 168579 A M + foo 168787 T W + foo 168959 A T - foo 169884 G S + foo 170032 G T - foo 172058 G K + foo 174942 A R + foo 175014 G K + foo 178406 G A - foo 179028 - A + foo 182394 C M + foo 182735 T Y + foo 183384 T K + foo 183893 - AT - foo 185360 G A - foo 185538 - G - foo 187948 G S + foo 188120 T G - foo 188179 T W + foo 188316 T Y + foo 189963 - G + foo 190093 C Y + foo 192220 C M + foo 192368 A W + foo 192782 T K + foo 193307 A R + foo 193501 G K + foo 194276 G S + foo 194930 C S + foo 196728 A W + foo 197559 G C - foo 198467 T W + foo 199042 C Y + foo 199259 AA - - foo 199687 TT - - foo 200287 C A - foo 200678 A R + foo 201208 C T - foo 201882 A - - foo 204456 T K + foo 206327 G R + foo 207311 G T - foo 209184 G A - foo 209279 C Y + foo 211459 C Y + foo 213807 T Y + foo 213846 T Y + foo 214635 A G - foo 214884 C A - foo 216244 A M + foo 216652 A M + foo 216745 T - - foo 216909 A T - foo 217579 A G - foo 217895 C Y + foo 218870 G K + foo 223098 T A - foo 223283 - C + foo 223666 C A - foo 224011 - C + foo 225681 C S + foo 227345 T C - foo 228778 T G - foo 229926 C - - foo 230778 T K + foo 230939 CG - - foo 231988 CT - - foo 234593 T W + foo 235496 C S + foo 235705 G K + foo 235758 A G - foo 236852 T C - foo 238790 A M + foo 238865 T K + foo 239329 A M + foo 239576 - C + foo 243058 G S + foo 244147 T - - foo 244462 C G - foo 245443 - A + foo 246544 C Y + foo 246744 T W + foo 247473 C M + foo 248129 C T - foo 249060 A C - foo 249515 G T - foo 250138 G S + foo 250567 C A - foo 254381 G R + foo 257864 C M + foo 257879 C Y + foo 259859 A M + foo 260643 C S + foo 261681 C G - foo 262645 T Y + foo 263279 A R + foo 263575 A - - foo 264587 - TA + foo 264689 T K + foo 265758 G K + foo 266272 A M + foo 268550 C M + foo 269986 G S + foo 270321 AC - - foo 273346 C S + foo 275367 C A - foo 277334 C G - foo 277629 G T - foo 278431 C Y + foo 281456 T Y + foo 281556 T G - foo 281737 G K + foo 282290 AC - - foo 282851 - C - foo 284405 A C - foo 288751 A C - foo 290501 TAAA - - foo 291315 A W + foo 291368 C - - foo 292154 A C - foo 292385 C M + foo 292555 G K + foo 297709 G C - foo 298183 A W + foo 298228 T W + foo 299902 T G - foo 302575 A T - foo 304823 G R + foo 305308 T Y + foo 305487 G S + foo 305697 G T - foo 306098 C G - foo 306882 T Y + foo 308201 A M + foo 308833 A T - foo 312033 A - - foo 312895 C G - foo 313889 C - - foo 315109 A R + foo 316083 C - - foo 316466 A R + foo 318040 G C - foo 319446 T C - foo 320236 C S + foo 320652 A - - foo 320716 T K + foo 323644 A - - foo 325359 G T - foo 329476 - CA + foo 329706 T G - foo 330181 T Y + foo 330703 C Y + foo 331315 G S + foo 332351 C A - foo 333408 A R + foo 333468 C S + foo 336247 A G - foo 336586 A M + foo 337364 G K + foo 337686 A T - foo 338043 A - - foo 338292 C G - foo 338962 A C - foo 339353 G K + foo 340647 - A + foo 341705 G R + foo 344283 C M + foo 345898 - AG - foo 347959 T - - foo 349162 C M + foo 352072 T Y + foo 354614 C Y + foo 359304 T - - foo 359312 - G + foo 360972 C S + foo 363857 C Y + foo 366226 A C - foo 367259 C M + foo 372502 T Y + foo 372747 A M + foo 375140 C S + foo 376298 T W + foo 376313 C - - foo 376760 T W + foo 378494 A W + foo 381137 T G - foo 381186 A R + foo 381701 A G - foo 382614 A W + foo 382761 C T - foo 382854 T C - foo 383201 C T - foo 385104 G S + foo 385233 - A + foo 386138 C T - foo 386316 A W + foo 387072 A R + foo 387642 - A + foo 388232 T C - foo 388890 GGG - - foo 390508 C S + foo 390625 C M + foo 391921 C G - foo 395256 G T - foo 395542 G S + foo 397015 A - - foo 397516 C Y + foo 397528 GC - - foo 398152 C T - foo 399802 A W + foo 400972 T K + foo 401419 - T + foo 401477 T W + foo 402437 A M + foo 402722 G R + foo 403452 C M + foo 404234 - A + foo 405344 A W + foo 407040 G S + foo 408483 G R + foo 408586 A C - foo 408721 A R + foo 409494 A M + foo 410078 A G - foo 411170 C A - foo 415342 T Y + foo 416265 C G - foo 417740 C A - foo 418622 C S + foo 420232 A W + foo 420288 T Y + foo 420908 A W + foo 421109 T A - foo 421357 A R + foo 422799 G A - foo 424383 C S + foo 424871 - GCA + foo 427273 T A - foo 429822 C M + foo 429846 T W + foo 432015 A G - foo 432414 G K + foo 433606 C Y + foo 433831 T Y + foo 437721 - A - foo 438402 G - - foo 438799 A T - foo 439422 C M + foo 440734 C A - foo 441840 T G - foo 442021 - C + foo 445021 T A - foo 445591 G A - foo 446138 T W + foo 447757 A W + foo 449156 T - - foo 449161 G K + foo 450114 A W + foo 450688 A W + foo 454421 C G - foo 454718 T Y + foo 455675 TC - - foo 461721 G R + foo 462526 G S + foo 467296 G A - foo 467510 G K + foo 468267 T K + foo 469118 G R + foo 469830 C Y + foo 471073 G T - foo 472056 G A - foo 472773 - A + foo 473046 G R + foo 473188 G A - foo 473742 C - - foo 474789 T A - foo 477763 G R + foo 478246 T W + foo 478975 T G - foo 479038 A R + foo 480275 T Y + foo 480317 G A - foo 481512 T K + foo 482069 G S + foo 482534 A R + foo 483760 C Y + foo 485281 T W + foo 486255 T C - foo 487038 T K + foo 487225 T A - foo 488012 C Y + foo 488795 T C - foo 490241 A R + foo 492595 - CGG + foo 493224 C A - foo 494284 A T - foo 495990 - T - foo 497306 A R + foo 497403 T Y + foo 499569 C Y + foo 499651 T K + foo 503139 T C - foo 504660 A R + foo 508679 C - - foo 513643 G K + foo 515668 CC - - foo 515836 G R + foo 516488 C S + foo 517602 G R + foo 517962 G K + foo 517975 T K + foo 519144 A T - foo 520068 T K + foo 520926 A W + foo 521562 C S + foo 522076 CG - - foo 522838 T Y + foo 523513 - C + foo 523907 - TA + foo 526271 T A - foo 526533 AC - - foo 526767 C Y + foo 528217 C Y + foo 531924 G S + foo 532333 - TT + foo 533132 C M + foo 534689 A T - foo 534779 A W + foo 535594 C A - foo 535795 G R + foo 538368 A R + foo 540879 G K + foo 542530 A - - foo 543620 G R + foo 544733 - C - foo 546300 - TT + foo 548196 A T - foo 548878 C M + foo 548885 G R + foo 549459 T K + foo 550908 A G - foo 551170 A - - foo 553130 T Y + foo 555293 T G - foo 556198 G R + foo 556355 A T - foo 557688 G K + foo 558415 G C - foo 558461 - G + foo 559287 T Y + foo 559465 C M + foo 560184 T W + foo 560252 T W + foo 562579 A M + foo 562961 G A - foo 566986 C A - foo 568134 C A - foo 569698 T C - foo 570180 T K + foo 570451 TG - - foo 570832 - A - foo 571589 A W + foo 572208 C M + foo 572871 C S + foo 574334 G - - foo 575673 T Y + foo 576797 G S + foo 578486 - C - foo 578494 C S + foo 579257 G A - foo 580103 G T - foo 580872 A W + foo 580925 G S + foo 580950 G C - foo 581637 T Y + foo 581654 A G - foo 582538 A T - foo 582691 C M + foo 582938 A W + foo 583104 T K + foo 584763 T W + foo 585723 T W + foo 588253 T Y + foo 588972 T C - foo 589438 - C - foo 591131 C Y + foo 591950 G R + foo 592194 T G - foo 592310 G S + foo 593892 G A - foo 598556 A - - foo 601660 G S + foo 602112 G T - foo 602412 T Y + foo 607282 - C + foo 607394 A M + foo 608438 A T - foo 609255 A W + foo 609365 - T + foo 611161 G K + foo 612224 C G - foo 614493 G R + foo 614601 G A - foo 614607 C Y + foo 619507 C M + foo 619798 T C - foo 621872 C T - foo 622375 C Y + foo 623208 - G - foo 624366 C A - foo 625320 - ACA - foo 626664 - G + foo 627140 T C - foo 627353 G T - foo 628714 T Y + foo 628744 A - - foo 629152 A G - foo 630110 T G - foo 631744 G K + foo 632763 C S + foo 634419 G - - foo 634459 A G - foo 634571 G A - foo 635366 - A + foo 635604 G T - foo 637057 T C - foo 637525 A T - foo 638412 A R + foo 640547 A W + foo 641514 T K + foo 642219 A R + foo 642427 A G - foo 642612 A R + foo 643553 T W + foo 647316 - T + foo 647598 C - - foo 651093 G A - foo 651718 G R + foo 652235 A G - foo 652579 A C - foo 653355 A W + foo 655174 C M + foo 655487 A M + foo 656849 G S + foo 661081 T K + foo 661134 G C - foo 661935 A W + foo 662010 A M + foo 662040 G R + foo 663030 A W + foo 663268 - C + foo 664991 T - - foo 665489 T K + foo 665555 C M + foo 665965 C Y + foo 668725 A C - foo 668834 - G - foo 668873 C S + foo 669654 T W + foo 671041 G S + foo 671485 T W + foo 671690 C M + foo 673022 G R + foo 674137 - T + foo 674782 A C - foo 676373 G T - foo 676793 T C - foo 677409 G S + foo 677536 - AA - foo 677620 G K + foo 677686 C Y + foo 678327 G S + foo 678704 G S + foo 678771 A C - foo 678866 C T - foo 679960 A W + foo 680447 - C + foo 682102 C T - foo 685497 T A - foo 686884 G S + foo 687324 ACA - - foo 687684 - AC + foo 687823 T C - foo 688590 G K + foo 690802 C M + foo 691388 T C - foo 691403 T G - foo 691790 G A - foo 692973 C A - foo 694058 G S + foo 694550 G R + foo 694968 T W + foo 695898 A T - foo 696721 C S + foo 696787 C S + foo 696935 A M + foo 698024 - C + foo 699813 A - - foo 700179 G R + foo 701421 A M + foo 701989 T A - foo 702862 C A - foo 707020 G A - foo 708420 A - - foo 708669 C G - foo 710521 T W + foo 711801 G C - foo 711913 T G - foo 715830 C M + foo 717664 TC - - foo 718845 A W + foo 719069 T Y + foo 719565 A W + foo 721136 T K + foo 726116 T K + foo 727809 T K + foo 728864 G K + foo 728918 G A - foo 730296 - T + foo 731988 C Y + foo 734658 A M + foo 734715 A W + foo 736618 C G - foo 737257 T Y + foo 740864 C A - foo 741640 G - - foo 741859 - TA - foo 742011 T K + foo 742237 A R + foo 742960 G K + foo 743731 G R + foo 743971 A W + foo 744635 T K + foo 746430 C G - foo 746489 - GC - foo 746881 C M + foo 756997 TC - - foo 757776 A M + foo 759870 A T - foo 760224 G K + foo 760799 G C - foo 761692 T C - foo 762569 G S + foo 763140 A G - foo 763842 - T - foo 764192 A M + foo 764334 G A - foo 764889 - AAT + foo 766464 G S + foo 768226 G A - foo 770272 T G - foo 771145 C Y + foo 772209 T A - foo 773672 T K + foo 773932 G C - foo 774658 C S + foo 775969 A M + foo 776816 T G - foo 777591 C Y + foo 777891 A M + foo 778164 C M + foo 778219 T W + foo 779260 G T - foo 779465 A W + foo 779779 G S + foo 780033 G K + foo 783243 C M + foo 783860 A R + foo 788345 A M + foo 789554 G - - foo 790025 G K + foo 791454 T K + foo 792009 C A - foo 792872 C G - foo 794616 T W + foo 795031 G R + foo 796919 C M + foo 797020 G S + foo 797042 G C - foo 797149 G A - foo 797177 A C - foo 799076 G C - foo 799580 G S + foo 800356 A R + foo 802297 G T - foo 802309 T Y + foo 802343 - C + foo 802769 A W + foo 803104 C G - foo 805819 C Y + foo 805972 T Y + foo 807503 T K + foo 807950 C M + foo 807994 - A - foo 809167 A G - foo 809658 A W + foo 810152 A M + foo 811506 G R + foo 813494 A M + foo 814035 G T - foo 814476 A W + foo 819399 T K + foo 820171 T W + foo 820445 G C - foo 822178 C G - foo 822504 C T - foo 823378 C M + foo 823591 CG - - foo 824229 C M + foo 824579 C T - foo 824858 C M + foo 826101 T K + foo 827593 C G - foo 827794 T Y + foo 828228 A M + foo 828367 T K + foo 828788 C M + foo 829002 C Y + foo 830345 C M + foo 831018 C A - foo 831459 T K + foo 832413 A T - foo 832782 T Y + foo 832908 T Y + foo 833130 T - - foo 833142 G S + foo 833241 G A - foo 836727 A T - foo 836829 G S + foo 838452 T G - foo 838543 A T - foo 838605 C M + foo 838954 G C - foo 841829 G K + foo 842324 - TC + foo 842996 - C + foo 844390 C A - foo 844793 A C - foo 844925 C A - foo 845082 G C - foo 846202 G R + foo 846707 A G - foo 848713 G A - foo 849372 C S + foo 849742 G A - foo 850499 C - - foo 850927 GT - - foo 851084 - G + foo 852247 A R + foo 852972 C A - foo 854808 T W + foo 855956 G K + foo 856225 G A - foo 856582 T K + foo 857351 C M + foo 857504 AC - - foo 858324 A T - foo 858858 T C - foo 859488 T Y + foo 862441 T Y + foo 863827 C Y + foo 864165 C A - foo 865997 C M + foo 866370 G S + foo 867653 G S + foo 867722 C Y + foo 868696 C M + foo 869005 T W + foo 869791 T Y + foo 875339 C Y + foo 875347 C M + foo 875584 T G - foo 876780 C T - foo 878368 A C - foo 878916 - CAG + foo 879005 A R + foo 880112 G T - foo 881021 - T - foo 881175 T W + foo 882168 - GGG + foo 882223 - G - foo 883033 TG - - foo 883381 C G - foo 884378 C - - foo 885075 A M + foo 885190 A W + foo 885568 A W + foo 885827 T Y + foo 887610 TG - - foo 889139 G R + foo 890978 T - - foo 891500 C Y + foo 892257 G C - foo 892642 G R + foo 892644 T W + foo 892757 C A - foo 893222 T - - foo 893348 T W + foo 894161 - C - foo 894447 A G - foo 894614 A W + foo 897817 T W + foo 899408 C S + foo 902450 A T - foo 902970 AT - - foo 905836 G K + foo 906524 GA - - foo 907484 A W + foo 907537 C M + foo 908515 G R + foo 908642 C T - foo 911145 T C - foo 912220 T Y + foo 912682 C Y + foo 914260 C S + foo 914757 T Y + foo 916413 G C - foo 916783 T G - foo 917033 G C - foo 917218 A - - foo 918225 G - - foo 918459 A - - foo 918732 A M + foo 919640 TC - - foo 920824 T W + foo 920836 G C - foo 924560 G R + foo 924659 GA - - foo 925868 T A - foo 928254 T G - foo 928369 - A - foo 928641 - AG + foo 929857 C M + foo 930211 T W + foo 930935 C T - foo 931986 A M + foo 932852 G T - foo 933965 T A - foo 935564 A W + foo 936034 T Y + foo 936221 AC - - foo 936670 C S + foo 936704 T A - foo 936786 T W + foo 939218 C S + foo 939312 A W + foo 939467 A W + foo 939934 C S + foo 941603 C Y + foo 942910 A W + foo 944654 T Y + foo 945301 A C - foo 945770 C T - foo 946078 G S + foo 948833 G K + foo 948999 A W + foo 949193 A R + foo 950276 C M + foo 950414 A W + foo 951285 G C - foo 953158 G R + foo 953287 A W + foo 954150 C G - foo 954258 G - - foo 955396 CC - - foo 956490 - AC + foo 958129 A R + foo 959027 T A - foo 959964 A W + foo 962042 A G - foo 962742 C G - foo 963306 T W + foo 963422 G K + foo 964082 G S + foo 965561 C S + foo 966531 T K + foo 967324 T W + foo 968419 - C - foo 969054 G - - foo 969158 G S + foo 972658 C M + foo 974266 T W + foo 974629 G K + foo 975034 A R + foo 975636 T W + foo 977078 - A - foo 978321 G T - foo 978595 C G - foo 979090 C M + foo 983855 TA - - foo 985725 T A - foo 988497 C Y + foo 990171 C M + foo 990804 - CA - foo 990941 T W + foo 991797 A W + foo 992469 A M + foo 994610 C Y + foo 998107 - T + foo 999725 G R + [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.5393.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.5393.smaltmap.smalt_index foo1.fasta # Reading sequences ... # Writing sequence set ... # Setting up hash index with collisions ... # word length = 13 bases, skip step = 2 bases ... # number of bits for key = 18 with 0 perfect bits # Counting keys ... # Counting k-tuples ... # Allocating k-tuple arrays ... # Counting k-tuple occurrences ... # Setting the k-tuple positions in index ... # Hash table is set up. # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Writing table to file ... # smalt: Total elapsed wall clock time: 0 seconds [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.5393.smaltmap.smalt_sample out.bam.tmp.5393.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.5393.smaltmap.smalt_sample out.bam.tmp.5393.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Check of read pairs ok ... # Mate names match ... # Sampling insert size distribution ... # Processed 9999 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:2 seconds # smalt: Total elapsed wall clock time: 2 seconds [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.5393.smaltmap.smalt_sample -f samsoft out.bam.tmp.5393.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.5393.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.5393.smaltmap.smalt_sample -f samsoft out.bam.tmp.5393.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Reading distribution of insert sizes from file ... # Sampled histogram # Smoothed histogram # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Processing query reads ... # Processed 10000 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:17 seconds # smalt: Total elapsed wall clock time: 17 seconds [REAPR smaltmap] Running: samtools sort out.bam.tmp.5393.smaltmap.raw.bam -O bam -o out.bam.tmp.5393.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.5393.smaltmap.raw.bam.sort.bam out.bam.tmp.5393.smaltmap.rmdup.bam [bam_rmdup_core] processing reference foo... [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.5393.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.5393.smaltmap.rmdup.bam >> out.bam.tmp.5393.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.5393.smaltmap.header out.bam.tmp.5393.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.5393.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck [REAPR pipeline] Running preprocess [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation [REAPR pipeline] Running stats [REAPR pipeline] Running fcdrate [REAPR pipeline] Running score [REAPR pipeline] Running break [REAPR pipeline] Running summary rm -rf /<>/debian/test make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mkdir -p debian/reapr/usr/lib/reapr install src/reapr.pl debian/reapr/usr/lib/reapr/reapr.pl chmod -x src/*.cpp find src -executable -exec install {} debian/reapr/usr/lib/reapr \; install: omitting directory 'src' dh_auto_install -- make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' for pl in `grep -Rl '#!/usr/bin/env' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' mkdir -p /<>/debian/man asciidoctor -a docdate='' -b manpage /<>/debian/man_src/*.adoc cp /<>/debian/man_src/*.? /<>/debian/man dh_installman -- make[1]: Leaving directory '/<>' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip debugedit: debian/reapr/usr/lib/reapr/task_stats: Unknown DWARF DW_FORM_0x1f20 1d80fc77d96071346fb7f047514406daca67c0a4 debugedit: debian/reapr/usr/lib/reapr/scaff2contig: Unknown DWARF DW_FORM_0x1f20 3054420a965e914769ec3645ea749a41de2a5eda debugedit: debian/reapr/usr/lib/reapr/bam2fragCov: Unknown DWARF DW_FORM_0x1f20 780e911c97846e8c0e67605d3c83706c25875705 debugedit: debian/reapr/usr/lib/reapr/task_break: Unknown DWARF DW_FORM_0x1f20 e4b709012c357f21e8cbe9d7b3e3876e96ab729e debugedit: debian/reapr/usr/lib/reapr/bam2insert: Unknown DWARF DW_FORM_0x1f20 4f50546aa78218a3570e114e86025d90eeedfd35 debugedit: debian/reapr/usr/lib/reapr/fa2gc: Unknown DWARF DW_FORM_0x1f20 29d8e86855ed14ae1331acf7991ff73470acbe8c debugedit: debian/reapr/usr/lib/reapr/bam2fcdEstimate: Unknown DWARF DW_FORM_0x1f21 33bbec8f0ec7f9394a03ba7802c7335fad0ab018 debugedit: debian/reapr/usr/lib/reapr/task_score: Unknown DWARF DW_FORM_0x1f20 d837c46137bb2b6a15dfe0cf6a8474e1f1cf6825 debugedit: debian/reapr/usr/lib/reapr/bam2perfect: Unknown DWARF DW_FORM_0x1f20 9c7dfd6f8ddeb3d795d5097e733a302afddda8b5 debugedit: debian/reapr/usr/lib/reapr/task_fcdrate: Unknown DWARF DW_FORM_0x1f20 38d7294d3b02034c8ea48514c1e19e4d95a36fd8 debugedit: debian/reapr/usr/lib/reapr/task_gapresize: Unknown DWARF DW_FORM_0x1f21 48815a479b698d0601a81b7239ddbad891f60e27 debugedit: debian/reapr/usr/lib/reapr/make_plots: Unknown DWARF DW_FORM_0x1f20 e49718f723481038a46771f458f7a417151f27b9 debugedit: debian/reapr/usr/lib/reapr/n50: Unknown DWARF DW_FORM_0x1f20 68eafeb1945e3d7b699550c7334bb6cadbae9be6 debugedit: debian/reapr/usr/lib/reapr/fa2gaps: Unknown DWARF DW_FORM_0x1f20 3c287836778ac5f204052ad93905d37f4e51016d dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 pkgstriptranslations: processing reapr (in debian/reapr); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/reapr/DEBIAN/control, package reapr, directory debian/reapr pkgstripfiles: Running PNG optimization (using 4 cpus) for package reapr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'reapr' in '../reapr_1.0.18+dfsg-5build1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../reapr_1.0.18+dfsg-5build1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../reapr_1.0.18+dfsg-5build1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-06-23T13:57:06Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ reapr_1.0.18+dfsg-5build1_amd64.changes: ---------------------------------------- Format: 1.8 Date: Tue, 24 Mar 2020 15:15:24 +0100 Source: reapr Binary: reapr Built-For-Profiles: noudeb Architecture: amd64 Version: 1.0.18+dfsg-5build1 Distribution: kinetic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: reapr - universal tool for genome assembly evaluation Changes: reapr (1.0.18+dfsg-5build1) focal; urgency=medium . * No-change rebuild for libgcc-s1 package name change. Checksums-Sha1: d3bc786abc0350347fac238cabfa633868a5b178 9420 reapr_1.0.18+dfsg-5build1_amd64.buildinfo 1601ef07b14a639103cd9210c09657704d2718cb 202140 reapr_1.0.18+dfsg-5build1_amd64.deb Checksums-Sha256: 211c72ae10efbf76c346c6fe70695520296773f63e4a37a592267089e5962a36 9420 reapr_1.0.18+dfsg-5build1_amd64.buildinfo 643dcb3a5ed6d28bfa62db3b0106cb33c7b09e67356ec876d25aac221ee2a42e 202140 reapr_1.0.18+dfsg-5build1_amd64.deb Files: 1e92a4d5dc1ed921b42ce7b84c5c504f 9420 science optional reapr_1.0.18+dfsg-5build1_amd64.buildinfo c369e11118de106fa76f7bc79ce3ed60 202140 science optional reapr_1.0.18+dfsg-5build1_amd64.deb /<>/reapr_1.0.18+dfsg-5build1_amd64.changes.new could not be renamed to /<>/reapr_1.0.18+dfsg-5build1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: reapr Binary: reapr Architecture: amd64 Version: 1.0.18+dfsg-5build1 Checksums-Md5: c369e11118de106fa76f7bc79ce3ed60 202140 reapr_1.0.18+dfsg-5build1_amd64.deb Checksums-Sha1: 1601ef07b14a639103cd9210c09657704d2718cb 202140 reapr_1.0.18+dfsg-5build1_amd64.deb Checksums-Sha256: 643dcb3a5ed6d28bfa62db3b0106cb33c7b09e67356ec876d25aac221ee2a42e 202140 reapr_1.0.18+dfsg-5build1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 23 Jun 2022 13:57:06 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: asciidoctor (= 2.0.16-2), autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), bamtools (= 2.5.1+dfsg-10build1), base-files (= 12.2ubuntu1), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38.50.20220615-4ubuntu1), binutils-common (= 2.38.50.20220615-4ubuntu1), binutils-x86-64-linux-gnu (= 2.38.50.20220615-4ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), ca-certificates (= 20211016), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-3ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.79ubuntu1), debhelper (= 13.7.1ubuntu1), debianutils (= 5.7-0.2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.8ubuntu1), dpkg-dev (= 1.21.8ubuntu1), dwz (= 0.14-1build2), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), fontconfig (= 2.13.1-4.4ubuntu1), fontconfig-config (= 2.13.1-4.4ubuntu1), fonts-dejavu-core (= 2.37-2build1), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.3.0-3ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.3.0-3ubuntu1), gcc-11-base (= 11.3.0-3ubuntu1), gcc-12-base (= 12.1.0-2ubuntu1), gettext (= 0.21-6), gettext-base (= 0.21-6), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hostname (= 3.23ubuntu2), init-system-helpers (= 1.63), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.3.0-3ubuntu1), libatomic1 (= 12.1.0-2ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libbambamc0 (= 0.0.50-6), libbamtools-dev (= 2.5.1+dfsg-10build1), libbamtools2.5.1 (= 2.5.1+dfsg-10build1), libbinutils (= 2.38.50.20220615-4ubuntu1), libblas3 (= 3.10.1-2), libblkid1 (= 2.38-4ubuntu1), libbrotli1 (= 1.0.9-2build6), libbsd0 (= 0.11.6-1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcairo2 (= 1.16.0-5ubuntu2), libcap-ng0 (= 0.7.9-4), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12.1.0-2ubuntu1), libcom-err2 (= 1.46.5-2ubuntu2), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38.50.20220615-4ubuntu1), libctf0 (= 2.38.50.20220615-4ubuntu1), libcurl3-gnutls (= 7.83.1-2), libcurl4 (= 7.83.1-2), libcurl4-gnutls-dev (= 7.83.1-2), libdatrie1 (= 0.2.13-2), libdb5.3 (= 5.3.28+dfsg1-0.9), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.7.1ubuntu1), libdeflate-dev (= 1.10-2), libdeflate0 (= 1.10-2), libdpkg-perl (= 1.21.8ubuntu1), libdw1 (= 0.187-1), libedit2 (= 3.1-20210910-1build1), libelf1 (= 0.187-1), libexpat1 (= 2.4.8-1), libffi8 (= 3.4.2-4), libfile-copy-link-perl (= 0.140-3), libfile-stripnondeterminism-perl (= 1.13.0-1), libfontconfig1 (= 2.13.1-4.4ubuntu1), libfreetype6 (= 2.12.1+dfsg-3), libfribidi0 (= 1.0.8-2ubuntu3.1), libgcc-11-dev (= 11.3.0-3ubuntu1), libgcc-s1 (= 12.1.0-2ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran5 (= 12.1.0-2ubuntu1), libglib2.0-0 (= 2.72.2-2), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgnutls30 (= 3.7.6-2ubuntu1), libgomp1 (= 12.1.0-2ubuntu1), libgpg-error0 (= 1.45-2), libgprofng0 (= 2.38.50.20220615-4ubuntu1), libgraphite2-3 (= 1.3.14-1build2), libgssapi-krb5-2 (= 1.19.2-2), libharfbuzz0b (= 2.7.4-1ubuntu4), libhogweed6 (= 3.7.3-1build2), libhts-dev (= 1.13+ds-2build2), libhts3 (= 1.13+ds-2build2), libhtscodecs2 (= 1.2.1-1), libice6 (= 2:1.0.10-1build2), libicu71 (= 71.1-3), libidn2-0 (= 2.3.2-2build1), libisl23 (= 0.24-2build1), libitm1 (= 12.1.0-2ubuntu1), libjbig0 (= 2.1-3.1build3), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu10), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-3ubuntu1), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), liblapack3 (= 3.10.1-2), libldap-2.5-0 (= 2.5.12+dfsg-2ubuntu1), liblsan0 (= 12.1.0-2ubuntu1), liblz4-1 (= 1.9.3-2build2), liblzma-dev (= 5.2.5-2.1), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-1build1), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libncurses6 (= 6.3+20220423-2), libnettle8 (= 3.7.3-1build2), libnghttp2-14 (= 1.47.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), libpam-runtime (= 1.4.0-13ubuntu1), libpam0g (= 1.4.0-13ubuntu1), libpango-1.0-0 (= 1.50.7+ds-1), libpangocairo-1.0-0 (= 1.50.7+ds-1), libpangoft2-1.0-0 (= 1.50.7+ds-1), libpaper-utils (= 1.1.28build2), libpaper1 (= 1.1.28build2), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-3ubuntu1), libpipeline1 (= 1.5.6-1), libpixman-1-0 (= 0.40.0-1build4), libpng16-16 (= 1.6.37-5), libpsl5 (= 0.21.0-1.2build2), libquadmath0 (= 12.1.0-2ubuntu1), libreadline8 (= 8.1.2-1.2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libruby3.0 (= 3.0.2-7ubuntu2), libsasl2-2 (= 2.1.28+dfsg-6ubuntu1), libsasl2-modules-db (= 2.1.28+dfsg-6ubuntu1), libseccomp2 (= 2.5.4-1ubuntu1), libselinux1 (= 3.4-1), libsigsegv2 (= 2.13-1ubuntu3), libsm6 (= 2:1.2.3-1build2), libsmartcols1 (= 2.38-4ubuntu1), libssh-4 (= 0.9.6-2build1), libssl3 (= 3.0.3-5ubuntu3), libstdc++-11-dev (= 11.3.0-3ubuntu1), libstdc++6 (= 12.1.0-2ubuntu1), libsub-override-perl (= 0.09-3), libsystemd0 (= 249.11-0ubuntu4), libtabixpp-dev (= 1.1.0-6), libtabixpp0 (= 1.1.0-6), libtasn1-6 (= 4.18.0-4build1), libtcl8.6 (= 8.6.12+dfsg-1build1), libthai-data (= 0.1.29-1build1), libthai0 (= 0.1.29-1build1), libtiff5 (= 4.4.0~rc1-1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtk8.6 (= 8.6.12-1build1), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-3ubuntu1), libubsan1 (= 12.1.0-2ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 249.11-0ubuntu4), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libwebp7 (= 1.2.2-2), libx11-6 (= 2:1.7.5-1), libx11-data (= 2:1.7.5-1), libxau6 (= 1:1.0.9-1build5), libxcb-render0 (= 1.14-3ubuntu3), libxcb-shm0 (= 1.14-3ubuntu3), libxcb1 (= 1.14-3ubuntu3), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxft2 (= 2.3.4-1), libxml2 (= 2.9.14+dfsg-1), libxrender1 (= 1:0.9.10-1.1), libxss1 (= 1:1.2.3-1build2), libxt6 (= 1:1.2.1-1), libyaml-0-2 (= 0.2.2-1build2), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-27.28), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 27), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), openssl (= 3.0.3-5ubuntu3), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), po-debconf (= 1.0.21+nmu1), r-base (= 4.2.0-1ubuntu1), r-base-core (= 4.2.0-1ubuntu1), r-cran-boot (= 1.3-28-2), r-cran-class (= 7.3-20-1), r-cran-cluster (= 2.1.3-1), r-cran-codetools (= 0.2-18-1), r-cran-foreign (= 0.8.82-1), r-cran-kernsmooth (= 2.23-20-1), r-cran-lattice (= 0.20-45-3), r-cran-mass (= 7.3-57-1), r-cran-matrix (= 1.4-1-1), r-cran-mgcv (= 1.8-40-1), r-cran-nlme (= 3.1.158-1), r-cran-nnet (= 7.3-17-1), r-cran-rpart (= 4.1.16-1), r-cran-spatial (= 7.3-15-1), r-cran-survival (= 3.3-1-1), r-recommended (= 4.2.0-1ubuntu1), rake (= 13.0.6-3), readline-common (= 8.1.2-1.2), rpcsvc-proto (= 1.4.2-0ubuntu6), ruby (= 1:3.0~exp1), ruby-asciidoctor (= 2.0.16-2), ruby-net-telnet (= 0.1.1-2.1), ruby-rubygems (= 3.3.15-1), ruby-webrick (= 1.7.0-3), ruby-xmlrpc (= 0.3.2-2), ruby3.0 (= 3.0.2-7ubuntu2), rubygems-integration (= 1.18), samtools (= 1.13-4), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), smalt (= 0.7.6-12), snpomatic (= 1.0-5), sysvinit-utils (= 3.01-1ubuntu1), tabix (= 1.13+ds-2build2), tar (= 1.34+dfsg-1build3), tzdata (= 2022a-0ubuntu1), ucf (= 3.0043), unzip (= 6.0-26ubuntu3), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), x11-common (= 1:7.7+23ubuntu2), xdg-utils (= 1.1.3-4.1ubuntu2), xz-utils (= 5.2.5-2.1), zip (= 3.0-12build2), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="noautodbgsym parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1585059324" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ reapr_1.0.18+dfsg-5build1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 202140 bytes: control archive=2083 bytes. 1522 bytes, 25 lines control 2623 bytes, 40 lines md5sums Package: reapr Version: 1.0.18+dfsg-5build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 794 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libstdc++6 (>= 11), libtabixpp0 (>= 1.0.0), samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl Section: science Priority: optional Homepage: https://www.sanger.ac.uk/science/tools/reapr Description: universal tool for genome assembly evaluation REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls. . The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly. drwxr-xr-x root/root 0 2020-03-24 14:15 ./ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/bin/ lrwxrwxrwx root/root 0 2020-03-24 14:15 ./usr/bin/reapr -> ../lib/reapr/reapr.pl drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/lib/ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/lib/reapr/ -rwxr-xr-x root/root 51600 2020-03-24 14:15 ./usr/lib/reapr/bam2fcdEstimate -rwxr-xr-x root/root 31120 2020-03-24 14:15 ./usr/lib/reapr/bam2fragCov -rwxr-xr-x root/root 59792 2020-03-24 14:15 ./usr/lib/reapr/bam2insert -rwxr-xr-x root/root 47504 2020-03-24 14:15 ./usr/lib/reapr/bam2perfect -rwxr-xr-x root/root 18824 2020-03-24 14:15 ./usr/lib/reapr/fa2gaps -rwxr-xr-x root/root 22920 2020-03-24 14:15 ./usr/lib/reapr/fa2gc -rwxr-xr-x root/root 31112 2020-03-24 14:15 ./usr/lib/reapr/make_plots -rwxr-xr-x root/root 31112 2020-03-24 14:15 ./usr/lib/reapr/n50 -rwxr-xr-x root/root 3505 2020-03-24 14:15 ./usr/lib/reapr/reapr.pl -rwxr-xr-x root/root 27016 2020-03-24 14:15 ./usr/lib/reapr/scaff2contig -rwxr-xr-x root/root 55696 2020-03-24 14:15 ./usr/lib/reapr/task_break -rwxr-xr-x root/root 2457 2020-03-24 14:15 ./usr/lib/reapr/task_facheck.pl -rwxr-xr-x root/root 51600 2020-03-24 14:15 ./usr/lib/reapr/task_fcdrate -rwxr-xr-x root/root 51600 2020-03-24 14:15 ./usr/lib/reapr/task_gapresize -rwxr-xr-x root/root 6007 2020-03-24 14:15 ./usr/lib/reapr/task_perfectfrombam.pl -rwxr-xr-x root/root 4471 2020-03-24 14:15 ./usr/lib/reapr/task_perfectmap.pl -rwxr-xr-x root/root 4060 2020-03-24 14:15 ./usr/lib/reapr/task_pipeline.pl -rwxr-xr-x root/root 3043 2020-03-24 14:15 ./usr/lib/reapr/task_plots.pl -rwxr-xr-x root/root 14801 2020-03-24 14:15 ./usr/lib/reapr/task_preprocess.pl -rwxr-xr-x root/root 137616 2020-03-24 14:15 ./usr/lib/reapr/task_score -rwxr-xr-x root/root 1373 2020-03-24 14:15 ./usr/lib/reapr/task_seqrename.pl -rwxr-xr-x root/root 5520 2020-03-24 14:15 ./usr/lib/reapr/task_smaltmap.pl -rwxr-xr-x root/root 96656 2020-03-24 14:15 ./usr/lib/reapr/task_stats -rwxr-xr-x root/root 8924 2020-03-24 14:15 ./usr/lib/reapr/task_summary.pl drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/share/ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/share/doc/reapr/ -rw-r--r-- root/root 798 2020-03-24 14:15 ./usr/share/doc/reapr/changelog.Debian.gz -rw-r--r-- root/root 1112 2019-12-26 15:22 ./usr/share/doc/reapr/copyright drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/share/man/ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/share/man/man1/ -rw-r--r-- root/root 924 2020-03-24 14:15 ./usr/share/man/man1/reapr-break.1.gz -rw-r--r-- root/root 613 2020-03-24 14:15 ./usr/share/man/man1/reapr-facheck.1.gz -rw-r--r-- root/root 506 2020-03-24 14:15 ./usr/share/man/man1/reapr-gapresize.1.gz -rw-r--r-- root/root 946 2020-03-24 14:15 ./usr/share/man/man1/reapr-perfectfrombam.1.gz -rw-r--r-- root/root 645 2020-03-24 14:15 ./usr/share/man/man1/reapr-perfectmap.1.gz -rw-r--r-- root/root 902 2020-03-24 14:15 ./usr/share/man/man1/reapr-pipeline.1.gz -rw-r--r-- root/root 496 2020-03-24 14:15 ./usr/share/man/man1/reapr-plots.1.gz -rw-r--r-- root/root 411 2020-03-24 14:15 ./usr/share/man/man1/reapr-preprocess.1.gz -rw-r--r-- root/root 937 2020-03-24 14:15 ./usr/share/man/man1/reapr-score.1.gz -rw-r--r-- root/root 476 2020-03-24 14:15 ./usr/share/man/man1/reapr-seqrename.1.gz -rw-r--r-- root/root 1027 2020-03-24 14:15 ./usr/share/man/man1/reapr-smaltmap.1.gz -rw-r--r-- root/root 749 2020-03-24 14:15 ./usr/share/man/man1/reapr-stats.1.gz -rw-r--r-- root/root 521 2020-03-24 14:15 ./usr/share/man/man1/reapr-summary.1.gz -rw-r--r-- root/root 1110 2020-03-24 14:15 ./usr/share/man/man1/reapr.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 54552 Build-Time: 181 Distribution: kinetic Host Architecture: amd64 Install-Time: 31 Job: reapr_1.0.18+dfsg-5build1.dsc Machine Architecture: amd64 Package: reapr Package-Time: 213 Source-Version: 1.0.18+dfsg-5build1 Space: 54552 Status: successful Version: 1.0.18+dfsg-5build1 -------------------------------------------------------------------------------- Finished at 2022-06-23T13:57:06Z Build needed 00:03:33, 54552k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24062841 Scanning for processes to kill in build PACKAGEBUILD-24062841