https://launchpad.net/ubuntu/+archive/test-rebuild-20180408/+build/14622629 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-s390x-010 4.4.0-121-generic #145-Ubuntu SMP Fri Apr 13 13:46:10 UTC 2018 s390x Buildd toolchain package versions: launchpad-buildd_161 python-lpbuildd_161 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 27 Apr 11:15:31 ntpdate[1755]: adjust time server 10.211.37.1 offset -0.002293 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=s390x PACKAGEBUILD-14622629 /home/buildd/filecache-default/17124f3eec304530bbb077109f97da7d4ad52147 Creating target for build PACKAGEBUILD-14622629 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=s390x PACKAGEBUILD-14622629 Starting target for build PACKAGEBUILD-14622629 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=s390x PACKAGEBUILD-14622629 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-14622629 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=s390x PACKAGEBUILD-14622629 Updating target for build PACKAGEBUILD-14622629 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main s390x Packages [943 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main Translation-en [516 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/universe s390x Packages [8175 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4941 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/multiverse s390x Packages [124 kB] Fetched 15.1 MB in 3s (4963 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14622629 s390x bionic -c chroot:build-PACKAGEBUILD-14622629 --arch=s390x --dist=bionic --nolog reapr_1.0.18+dfsg-3.dsc Initiating build PACKAGEBUILD-14622629 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-121-generic #145-Ubuntu SMP Fri Apr 13 13:46:10 UTC 2018 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-010.buildd +==============================================================================+ | reapr 1.0.18+dfsg-3 (s390x) 27 Apr 2018 11:15 | +==============================================================================+ Package: reapr Version: 1.0.18+dfsg-3 Source Version: 1.0.18+dfsg-3 Distribution: bionic Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/reapr-p08D9f/reapr-1.0.18+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/reapr-p08D9f' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14622629/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- reapr_1.0.18+dfsg-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-wpcWaY/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-wpcWaY/apt_archive ./ InRelease Get:2 copy:/<>/resolver-wpcWaY/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-wpcWaY/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-wpcWaY/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-wpcWaY/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (274 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-wpcWaY/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12382 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl Filtered Build-Depends: debhelper (>= 9), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl dpkg-deb: building package 'sbuild-build-depends-reapr-dummy' in '/<>/resolver-dEqdP5/apt_archive/sbuild-build-depends-reapr-dummy.deb'. Ign:1 copy:/<>/resolver-dEqdP5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-dEqdP5/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-dEqdP5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-dEqdP5/apt_archive ./ Sources [288 B] Get:5 copy:/<>/resolver-dEqdP5/apt_archive ./ Packages [605 B] Fetched 3012 B in 0s (282 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install reapr 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 bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbambamc0 libbamtools-dev libbamtools2.4.0 libblas3 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran4 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libice6 libicu60 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtool libwind0-heimdal 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-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.5 rubygems-integration samtools smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc krb5-doc krb5-user liblzma-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl ess r-doc-info | r-doc-pdf r-mathlib r-base-html ri ruby-dev bundler Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-base-html r-doc-html r-base-dev fonts-lato libjs-jquery python cwltool 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 bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbambamc0 libbamtools-dev libbamtools2.4.0 libblas3 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran4 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libice6 libicu60 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtool libwind0-heimdal 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-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.5 rubygems-integration samtools sbuild-build-depends-reapr-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 72.0 MB of archives. After this operation, 191 MB of additional disk space will be used. Get:1 copy:/<>/resolver-dEqdP5/apt_archive ./ sbuild-build-depends-reapr-dummy 0.invalid.0 [940 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main s390x libbsd0 s390x 0.8.7-1 [40.0 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main s390x bsdmainutils s390x 11.1.2ubuntu1 [181 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main s390x groff-base s390x 1.22.3-10 [1174 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main s390x libpipeline1 s390x 1.5.0-1 [24.1 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main s390x man-db s390x 2.8.3-2 [1007 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main s390x libexpat1 s390x 2.2.5-3 [79.3 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main s390x libfreetype6 s390x 2.8.1-2ubuntu2 [314 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main s390x ucf all 3.0038 [50.5 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main s390x fonts-dejavu-core all 2.37-1 [1041 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main s390x fontconfig-config all 2.12.6-0ubuntu2 [55.8 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main s390x libfontconfig1 s390x 2.12.6-0ubuntu2 [132 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main s390x fontconfig s390x 2.12.6-0ubuntu2 [168 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main s390x libjpeg-turbo8 s390x 1.5.2-0ubuntu5 [100 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main s390x libmagic-mgc s390x 1:5.32-2 [185 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main s390x libmagic1 s390x 1:5.32-2 [66.9 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main s390x file s390x 1:5.32-2 [21.9 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main s390x libglib2.0-0 s390x 2.56.1-2ubuntu1 [1077 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main s390x libicu60 s390x 60.2-3ubuntu3 [7837 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main s390x libxml2 s390x 2.9.4+dfsg1-6.1ubuntu1 [587 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main s390x libyaml-0-2 s390x 0.1.7-2ubuntu3 [41.3 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main s390x gettext-base s390x 0.19.8.1-6 [48.3 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main s390x libkrb5support0 s390x 1.16-2build1 [30.4 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main s390x libk5crypto3 s390x 1.16-2build1 [84.1 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main s390x libkeyutils1 s390x 1.5.9-9.2ubuntu2 [8520 B] Get:26 http://ftpmaster.internal/ubuntu bionic/main s390x libkrb5-3 s390x 1.16-2build1 [261 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main s390x libgssapi-krb5-2 s390x 1.16-2build1 [110 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main s390x libpsl5 s390x 0.19.1-5build1 [41.5 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main s390x libxau6 s390x 1:1.0.8-1 [7420 B] Get:30 http://ftpmaster.internal/ubuntu bionic/main s390x libxdmcp6 s390x 1:1.1.2-3 [10.7 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main s390x libxcb1 s390x 1.13-1 [43.6 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main s390x libx11-data all 2:1.6.4-3 [114 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main s390x libx11-6 s390x 2:1.6.4-3 [546 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main s390x libxext6 s390x 2:1.3.3-1 [27.8 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main s390x rubygems-integration all 1.11 [4994 B] Get:36 http://ftpmaster.internal/ubuntu bionic/main s390x rake all 12.3.1-1 [45.1 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main s390x ruby-did-you-mean all 1.2.0-2 [9700 B] Get:38 http://ftpmaster.internal/ubuntu bionic/main s390x ruby-minitest all 5.10.3-1 [38.6 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main s390x ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main s390x ruby-power-assert all 0.3.0-1 [7952 B] Get:41 http://ftpmaster.internal/ubuntu bionic/main s390x ruby-test-unit all 3.2.5-1 [61.1 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main s390x libruby2.5 s390x 2.5.1-1ubuntu1 [2967 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main s390x ruby2.5 s390x 2.5.1-1ubuntu1 [48.6 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main s390x ruby s390x 1:2.5.1 [5712 B] Get:45 http://ftpmaster.internal/ubuntu bionic/universe s390x asciidoctor all 1.5.5-1 [168 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main s390x libsigsegv2 s390x 2.12-1 [14.6 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main s390x m4 s390x 1.4.18-1 [195 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main s390x autoconf all 2.69-11 [322 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main s390x autotools-dev all 20180224.1 [39.6 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main s390x automake all 1:1.15.1-3ubuntu2 [509 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main s390x autopoint all 0.19.8.1-6 [412 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/universe s390x libbamtools2.4.0 s390x 2.4.1+dfsg-2 [165 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main s390x libjsoncpp1 s390x 1.7.4-3 [70.8 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/universe s390x bamtools s390x 2.4.1+dfsg-2 [183 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main s390x libtool all 2.4.6-2 [194 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main s390x dh-autoreconf all 17 [15.8 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main s390x libarchive-zip-perl all 1.60-1 [83.9 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main s390x libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main s390x dh-strip-nondeterminism all 0.040-1.1~build1 [5208 B] Get:61 http://ftpmaster.internal/ubuntu bionic/main s390x libcroco3 s390x 0.6.12-2 [74.2 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main s390x gettext s390x 0.19.8.1-6 [858 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main s390x po-debconf all 1.0.20 [232 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main s390x debhelper all 11.1.6ubuntu1 [902 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main s390x libroken18-heimdal s390x 7.5.0+dfsg-1 [39.4 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main s390x libasn1-8-heimdal s390x 7.5.0+dfsg-1 [147 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/universe s390x libbambamc0 s390x 0.0.50-1 [34.6 kB] Get:69 http://ftpmaster.internal/ubuntu bionic/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-0ubuntu2 [173 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/universe s390x libbamtools-dev s390x 2.4.1+dfsg-2 [211 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main s390x libblas3 s390x 3.7.1-4ubuntu1 [119 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main s390x libpixman-1-0 s390x 0.34.0-2 [135 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main s390x libxcb-render0 s390x 1.13-1 [14.7 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main s390x libxcb-shm0 s390x 1.13-1 [5528 B] Get:75 http://ftpmaster.internal/ubuntu bionic/main s390x libxrender1 s390x 1:0.9.10-1 [17.8 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main s390x libcairo2 s390x 1.15.10-2 [533 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main s390x libheimbase1-heimdal s390x 7.5.0+dfsg-1 [27.5 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main s390x libhcrypto4-heimdal s390x 7.5.0+dfsg-1 [82.4 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main s390x libwind0-heimdal s390x 7.5.0+dfsg-1 [47.7 kB] Get:80 http://ftpmaster.internal/ubuntu bionic/main s390x libhx509-5-heimdal s390x 7.5.0+dfsg-1 [98.3 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main s390x libkrb5-26-heimdal s390x 7.5.0+dfsg-1 [190 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main s390x libheimntlm0-heimdal s390x 7.5.0+dfsg-1 [14.1 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main s390x libgssapi3-heimdal s390x 7.5.0+dfsg-1 [86.9 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main s390x libsasl2-modules-db s390x 2.1.27~101-g0780600+dfsg-3ubuntu2 [13.9 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main s390x libsasl2-2 s390x 2.1.27~101-g0780600+dfsg-3ubuntu2 [46.5 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main s390x libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main s390x libldap-2.4-2 s390x 2.4.45+dfsg-1ubuntu1 [144 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main s390x libnghttp2-14 s390x 1.30.0-1ubuntu1 [74.1 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-1 [51.8 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main s390x libcurl3-gnutls s390x 7.58.0-2ubuntu3 [195 kB] Get:91 http://ftpmaster.internal/ubuntu bionic/main s390x libcurl4 s390x 7.58.0-2ubuntu3 [196 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main s390x libdatrie1 s390x 0.2.10-7 [17.5 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/universe s390x libfile-copy-link-perl all 0.140-2 [15.2 kB] Get:94 http://ftpmaster.internal/ubuntu bionic/main s390x libgfortran4 s390x 7.3.0-16ubuntu3 [275 kB] Get:95 http://ftpmaster.internal/ubuntu bionic/main s390x libgraphite2-3 s390x 1.3.11-2 [71.3 kB] Get:96 http://ftpmaster.internal/ubuntu bionic/main s390x libharfbuzz0b s390x 1.7.2-1ubuntu1 [218 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/universe s390x libhts2 s390x 1.7-2 [278 kB] Get:98 http://ftpmaster.internal/ubuntu bionic/main s390x liblzma-dev s390x 5.2.2-1.3 [145 kB] Get:99 http://ftpmaster.internal/ubuntu bionic/universe s390x libhts-dev s390x 1.7-2 [360 kB] Get:100 http://ftpmaster.internal/ubuntu bionic/main s390x x11-common all 1:7.7+19ubuntu7 [22.0 kB] Get:101 http://ftpmaster.internal/ubuntu bionic/main s390x libice6 s390x 2:1.0.9-2 [36.9 kB] Get:102 http://ftpmaster.internal/ubuntu bionic/main s390x libjpeg8 s390x 8c-2ubuntu8 [2142 B] Get:103 http://ftpmaster.internal/ubuntu bionic/main s390x liblapack3 s390x 3.7.1-4ubuntu1 [1621 kB] Get:104 http://ftpmaster.internal/ubuntu bionic/main s390x libthai-data all 0.1.27-2 [133 kB] Get:105 http://ftpmaster.internal/ubuntu bionic/main s390x libthai0 s390x 0.1.27-2 [18.2 kB] Get:106 http://ftpmaster.internal/ubuntu bionic/main s390x libpango-1.0-0 s390x 1.40.14-1 [148 kB] Get:107 http://ftpmaster.internal/ubuntu bionic/main s390x libpangoft2-1.0-0 s390x 1.40.14-1 [31.5 kB] Get:108 http://ftpmaster.internal/ubuntu bionic/main s390x libpangocairo-1.0-0 s390x 1.40.14-1 [19.2 kB] Get:109 http://ftpmaster.internal/ubuntu bionic/main s390x libpaper1 s390x 1.1.24+nmu5ubuntu1 [13.5 kB] Get:110 http://ftpmaster.internal/ubuntu bionic/main s390x libpaper-utils s390x 1.1.24+nmu5ubuntu1 [8182 B] Get:111 http://ftpmaster.internal/ubuntu bionic/main s390x libsm6 s390x 2:1.2.2-1 [15.3 kB] Get:112 http://ftpmaster.internal/ubuntu bionic/universe s390x libtabixpp0 s390x 1.0.0-3build2 [7768 B] Get:113 http://ftpmaster.internal/ubuntu bionic/universe s390x libtabixpp-dev s390x 1.0.0-3build2 [6474 B] Get:114 http://ftpmaster.internal/ubuntu bionic/main s390x libtcl8.6 s390x 8.6.8+dfsg-3 [817 kB] Get:115 http://ftpmaster.internal/ubuntu bionic/main s390x libjbig0 s390x 2.1-3.1build1 [26.3 kB] Get:116 http://ftpmaster.internal/ubuntu bionic/main s390x libtiff5 s390x 4.0.9-5 [142 kB] Get:117 http://ftpmaster.internal/ubuntu bionic/main s390x libxft2 s390x 2.3.2-1 [36.7 kB] Get:118 http://ftpmaster.internal/ubuntu bionic/main s390x libxss1 s390x 1:1.2.2-1 [7602 B] Get:119 http://ftpmaster.internal/ubuntu bionic/main s390x libtk8.6 s390x 8.6.8-4 [650 kB] Get:120 http://ftpmaster.internal/ubuntu bionic/main s390x libxt6 s390x 1:1.1.5-1 [147 kB] Get:121 http://ftpmaster.internal/ubuntu bionic/main s390x zip s390x 3.0-11build1 [157 kB] Get:122 http://ftpmaster.internal/ubuntu bionic/main s390x unzip s390x 6.0-21ubuntu1 [156 kB] Get:123 http://ftpmaster.internal/ubuntu bionic/main s390x xdg-utils all 1.1.2-1ubuntu2 [60.7 kB] Get:124 http://ftpmaster.internal/ubuntu bionic/universe s390x r-base-core s390x 3.4.4-1ubuntu1 [23.0 MB] Get:125 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-boot all 1.3-20-1.1 [613 kB] Get:126 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-cluster s390x 2.0.6-2build1 [500 kB] Get:127 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-foreign s390x 0.8.69-1build1 [226 kB] Get:128 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-mass s390x 7.3-49-1 [1099 kB] Get:129 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-kernsmooth s390x 2.23-15-3build1 [89.0 kB] Get:130 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-lattice s390x 0.20-35-1build1 [712 kB] Get:131 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-nlme s390x 3.1.131-3build1 [2175 kB] Get:132 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-matrix s390x 1.2-12-1 [2321 kB] Get:133 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-mgcv s390x 1.8-23-1 [2484 kB] Get:134 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-survival s390x 2.41-3-2build1 [5148 kB] Get:135 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-rpart s390x 4.1-13-1 [879 kB] Get:136 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-class s390x 7.3-14-2build1 [86.4 kB] Get:137 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-nnet s390x 7.3-12-2build1 [110 kB] Get:138 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-spatial s390x 7.3-11-2build1 [126 kB] Get:139 http://ftpmaster.internal/ubuntu bionic/universe s390x r-cran-codetools all 0.2-15-1.1 [46.1 kB] Get:140 http://ftpmaster.internal/ubuntu bionic/universe s390x r-recommended all 3.4.4-1ubuntu1 [2820 B] Get:141 http://ftpmaster.internal/ubuntu bionic/universe s390x r-base all 3.4.4-1ubuntu1 [9312 B] Get:142 http://ftpmaster.internal/ubuntu bionic/universe s390x samtools s390x 1.7-1 [268 kB] Get:143 http://ftpmaster.internal/ubuntu bionic/universe s390x smalt s390x 0.7.6-7 [107 kB] Get:144 http://ftpmaster.internal/ubuntu bionic/universe s390x snpomatic s390x 1.0-3 [80.0 kB] Get:145 http://ftpmaster.internal/ubuntu bionic/universe s390x tabix s390x 1.7-2 [297 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 72.0 MB in 3s (20.6 MB/s) Selecting previously unselected package libbsd0:s390x. (Reading database ... 12382 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.8.7-1_s390x.deb ... Unpacking libbsd0:s390x (0.8.7-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2ubuntu1_s390x.deb ... Unpacking bsdmainutils (11.1.2ubuntu1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.3-10_s390x.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../003-libpipeline1_1.5.0-1_s390x.deb ... Unpacking libpipeline1:s390x (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.8.3-2_s390x.deb ... Unpacking man-db (2.8.3-2) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../005-libexpat1_2.2.5-3_s390x.deb ... Unpacking libexpat1:s390x (2.2.5-3) ... 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Unpacking fontconfig (2.12.6-0ubuntu2) ... Selecting previously unselected package libjpeg-turbo8:s390x. Preparing to unpack .../012-libjpeg-turbo8_1.5.2-0ubuntu5_s390x.deb ... Unpacking libjpeg-turbo8:s390x (1.5.2-0ubuntu5) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../013-libmagic-mgc_1%3a5.32-2_s390x.deb ... Unpacking libmagic-mgc (1:5.32-2) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../014-libmagic1_1%3a5.32-2_s390x.deb ... Unpacking libmagic1:s390x (1:5.32-2) ... Selecting previously unselected package file. Preparing to unpack .../015-file_1%3a5.32-2_s390x.deb ... Unpacking file (1:5.32-2) ... Selecting previously unselected package libglib2.0-0:s390x. Preparing to unpack .../016-libglib2.0-0_2.56.1-2ubuntu1_s390x.deb ... Unpacking libglib2.0-0:s390x (2.56.1-2ubuntu1) ... Selecting previously unselected package libicu60:s390x. Preparing to unpack .../017-libicu60_60.2-3ubuntu3_s390x.deb ... Unpacking libicu60:s390x (60.2-3ubuntu3) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../018-libxml2_2.9.4+dfsg1-6.1ubuntu1_s390x.deb ... Unpacking libxml2:s390x (2.9.4+dfsg1-6.1ubuntu1) ... Selecting previously unselected package libyaml-0-2:s390x. Preparing to unpack .../019-libyaml-0-2_0.1.7-2ubuntu3_s390x.deb ... Unpacking libyaml-0-2:s390x (0.1.7-2ubuntu3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../020-gettext-base_0.19.8.1-6_s390x.deb ... Unpacking gettext-base (0.19.8.1-6) ... Selecting previously unselected package libkrb5support0:s390x. Preparing to unpack .../021-libkrb5support0_1.16-2build1_s390x.deb ... Unpacking libkrb5support0:s390x (1.16-2build1) ... Selecting previously unselected package libk5crypto3:s390x. Preparing to unpack .../022-libk5crypto3_1.16-2build1_s390x.deb ... Unpacking libk5crypto3:s390x (1.16-2build1) ... Selecting previously unselected package libkeyutils1:s390x. 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Unpacking libcroco3:s390x (0.6.12-2) ... Selecting previously unselected package gettext. Preparing to unpack .../060-gettext_0.19.8.1-6_s390x.deb ... Unpacking gettext (0.19.8.1-6) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../061-intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../062-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../063-debhelper_11.1.6ubuntu1_all.deb ... Unpacking debhelper (11.1.6ubuntu1) ... Selecting previously unselected package libroken18-heimdal:s390x. Preparing to unpack .../064-libroken18-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libroken18-heimdal:s390x (7.5.0+dfsg-1) ... Selecting previously unselected package libasn1-8-heimdal:s390x. Preparing to unpack .../065-libasn1-8-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libasn1-8-heimdal:s390x (7.5.0+dfsg-1) ... Selecting previously unselected package libbambamc0. Preparing to unpack .../066-libbambamc0_0.0.50-1_s390x.deb ... Unpacking libbambamc0 (0.0.50-1) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../067-zlib1g-dev_1%3a1.2.11.dfsg-0ubuntu2_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.2.11.dfsg-0ubuntu2) ... Selecting previously unselected package libbamtools-dev. Preparing to unpack .../068-libbamtools-dev_2.4.1+dfsg-2_s390x.deb ... Unpacking libbamtools-dev (2.4.1+dfsg-2) ... Selecting previously unselected package libblas3:s390x. Preparing to unpack .../069-libblas3_3.7.1-4ubuntu1_s390x.deb ... Unpacking libblas3:s390x (3.7.1-4ubuntu1) ... Selecting previously unselected package libpixman-1-0:s390x. Preparing to unpack .../070-libpixman-1-0_0.34.0-2_s390x.deb ... Unpacking libpixman-1-0:s390x (0.34.0-2) ... Selecting previously unselected package libxcb-render0:s390x. Preparing to unpack .../071-libxcb-render0_1.13-1_s390x.deb ... Unpacking libxcb-render0:s390x (1.13-1) ... Selecting previously unselected package libxcb-shm0:s390x. Preparing to unpack .../072-libxcb-shm0_1.13-1_s390x.deb ... Unpacking libxcb-shm0:s390x (1.13-1) ... Selecting previously unselected package libxrender1:s390x. Preparing to unpack .../073-libxrender1_1%3a0.9.10-1_s390x.deb ... Unpacking libxrender1:s390x (1:0.9.10-1) ... Selecting previously unselected package libcairo2:s390x. Preparing to unpack .../074-libcairo2_1.15.10-2_s390x.deb ... Unpacking libcairo2:s390x (1.15.10-2) ... Selecting previously unselected package libheimbase1-heimdal:s390x. Preparing to unpack .../075-libheimbase1-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libheimbase1-heimdal:s390x (7.5.0+dfsg-1) ... Selecting previously unselected package libhcrypto4-heimdal:s390x. Preparing to unpack .../076-libhcrypto4-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libhcrypto4-heimdal:s390x (7.5.0+dfsg-1) ... Selecting previously unselected package libwind0-heimdal:s390x. Preparing to unpack .../077-libwind0-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libwind0-heimdal:s390x (7.5.0+dfsg-1) ... Selecting previously unselected package libhx509-5-heimdal:s390x. Preparing to unpack .../078-libhx509-5-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libhx509-5-heimdal:s390x (7.5.0+dfsg-1) ... Selecting previously unselected package libkrb5-26-heimdal:s390x. Preparing to unpack .../079-libkrb5-26-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libkrb5-26-heimdal:s390x (7.5.0+dfsg-1) ... Selecting previously unselected package libheimntlm0-heimdal:s390x. Preparing to unpack .../080-libheimntlm0-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libheimntlm0-heimdal:s390x (7.5.0+dfsg-1) ... Selecting previously unselected package libgssapi3-heimdal:s390x. Preparing to unpack .../081-libgssapi3-heimdal_7.5.0+dfsg-1_s390x.deb ... Unpacking libgssapi3-heimdal:s390x (7.5.0+dfsg-1) ... 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Unpacking r-recommended (3.4.4-1ubuntu1) ... Selecting previously unselected package r-base. Preparing to unpack .../139-r-base_3.4.4-1ubuntu1_all.deb ... Unpacking r-base (3.4.4-1ubuntu1) ... Selecting previously unselected package samtools. Preparing to unpack .../140-samtools_1.7-1_s390x.deb ... Unpacking samtools (1.7-1) ... Selecting previously unselected package smalt. Preparing to unpack .../141-smalt_0.7.6-7_s390x.deb ... Unpacking smalt (0.7.6-7) ... Selecting previously unselected package snpomatic. Preparing to unpack .../142-snpomatic_1.0-3_s390x.deb ... Unpacking snpomatic (1.0-3) ... Selecting previously unselected package tabix. Preparing to unpack .../143-tabix_1.7-2_s390x.deb ... Unpacking tabix (1.7-2) ... Selecting previously unselected package sbuild-build-depends-reapr-dummy. Preparing to unpack .../144-sbuild-build-depends-reapr-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-reapr-dummy (0.invalid.0) ... Setting up libexpat1:s390x (2.2.5-3) ... Setting up libicu60:s390x (60.2-3ubuntu3) ... Setting up libarchive-zip-perl (1.60-1) ... Setting up libnghttp2-14:s390x (1.30.0-1ubuntu1) ... Setting up libgfortran4:s390x (7.3.0-16ubuntu3) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libjbig0:s390x (2.1-3.1build1) ... Setting up libsigsegv2:s390x (2.12-1) ... Setting up libldap-common (2.4.45+dfsg-1ubuntu1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libbamtools2.4.0 (2.4.1+dfsg-2) ... Setting up libpsl5:s390x (0.19.1-5build1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:s390x (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:s390x (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up unzip (6.0-21ubuntu1) ... Setting up libsasl2-2:s390x (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libdatrie1:s390x (0.2.10-7) ... Setting up gettext-base (0.19.8.1-6) ... Setting up libjpeg-turbo8:s390x (1.5.2-0ubuntu5) ... Setting up libpipeline1:s390x (1.5.0-1) ... Setting up libroken18-heimdal:s390x (7.5.0+dfsg-1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:s390x (0.8.7-1) ... Setting up libkrb5support0:s390x (1.16-2build1) ... Setting up ucf (3.0038) ... Setting up libxml2:s390x (2.9.4+dfsg1-6.1ubuntu1) ... Setting up zip (3.0-11build1) ... Setting up libfreetype6:s390x (2.8.1-2ubuntu2) ... Setting up libmagic-mgc (1:5.32-2) ... Setting up libmagic1:s390x (1:5.32-2) ... Setting up libgraphite2-3:s390x (1.3.11-2) ... Setting up libcroco3:s390x (0.6.12-2) ... Setting up ruby-did-you-mean (1.2.0-2) ... Setting up libyaml-0-2:s390x (0.1.7-2ubuntu3) ... Setting up libpixman-1-0:s390x (0.34.0-2) ... Setting up libblas3:s390x (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:s390x (7.5.0+dfsg-1) ... Processing triggers for systemd (237-3ubuntu10) ... Setting up snpomatic (1.0-3) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up rubygems-integration (1.11) ... Setting up libbambamc0 (0.0.50-1) ... Setting up libtcl8.6:s390x (8.6.8+dfsg-3) ... Setting up libthai-data (0.1.27-2) ... Setting up liblzma-dev:s390x (5.2.2-1.3) ... Setting up libxdmcp6:s390x (1:1.1.2-3) ... Setting up libkeyutils1:s390x (1.5.9-9.2ubuntu2) ... Setting up bsdmainutils (11.1.2ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up ruby-minitest (5.10.3-1) ... Setting up x11-common (1:7.7+19ubuntu7) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.2-1ubuntu2) ... Setting up libfile-copy-link-perl (0.140-2) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libxau6:s390x (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-6) ... Setting up ruby-power-assert (0.3.0-1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ... Setting up libjpeg8:s390x (8c-2ubuntu8) ... Setting up libjsoncpp1:s390x (1.7.4-3) ... Setting up libpaper1:s390x (1.1.24+nmu5ubuntu1) ... Creating config file /etc/papersize with new version Setting up libk5crypto3:s390x (1.16-2build1) ... Setting up libpaper-utils (1.1.24+nmu5ubuntu1) ... Setting up fontconfig-config (2.12.6-0ubuntu2) ... Setting up libwind0-heimdal:s390x (7.5.0+dfsg-1) ... Setting up gettext (0.19.8.1-6) ... Setting up libasn1-8-heimdal:s390x (7.5.0+dfsg-1) ... Setting up liblapack3:s390x (3.7.1-4ubuntu1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode Setting up libbamtools-dev (2.4.1+dfsg-2) ... Setting up libhcrypto4-heimdal:s390x (7.5.0+dfsg-1) ... Setting up bamtools (2.4.1+dfsg-2) ... Setting up libharfbuzz0b:s390x (1.7.2-1ubuntu1) ... Setting up libtiff5:s390x (4.0.9-5) ... Setting up autoconf (2.69-11) ... Setting up libthai0:s390x (0.1.27-2) ... Setting up file (1:5.32-2) ... Setting up libhx509-5-heimdal:s390x (7.5.0+dfsg-1) ... Setting up smalt (0.7.6-7) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up libice6:s390x (2:1.0.9-2) ... Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:s390x (1.16-2build1) ... Setting up libkrb5-26-heimdal:s390x (7.5.0+dfsg-1) ... Setting up libxcb1:s390x (1.13-1) ... Setting up libheimntlm0-heimdal:s390x (7.5.0+dfsg-1) ... Setting up libtool (2.4.6-2) ... Setting up libfontconfig1:s390x (2.12.6-0ubuntu2) ... Setting up libsm6:s390x (2:1.2.2-1) ... Setting up libxcb-render0:s390x (1.13-1) ... Setting up po-debconf (1.0.20) ... Setting up libx11-6:s390x (2:1.6.4-3) ... Setting up libgssapi-krb5-2:s390x (1.16-2build1) ... Setting up libxcb-shm0:s390x (1.13-1) ... Setting up libxt6:s390x (1:1.1.5-1) ... Setting up libxrender1:s390x (1:0.9.10-1) ... Setting up libxft2:s390x (2.3.2-1) ... Setting up libgssapi3-heimdal:s390x (7.5.0+dfsg-1) ... Setting up fontconfig (2.12.6-0ubuntu2) ... Regenerating fonts cache... done. Setting up libxext6:s390x (2:1.3.3-1) ... Setting up libxss1:s390x (1:1.2.2-1) ... Setting up libldap-2.4-2:s390x (2.4.45+dfsg-1ubuntu1) ... Setting up libpango-1.0-0:s390x (1.40.14-1) ... Setting up libcairo2:s390x (1.15.10-2) ... Setting up libcurl3-gnutls:s390x (7.58.0-2ubuntu3) ... Setting up libtk8.6:s390x (8.6.8-4) ... Setting up libcurl4:s390x (7.58.0-2ubuntu3) ... Setting up libpangoft2-1.0-0:s390x (1.40.14-1) ... Setting up tabix (1.7-2) ... Setting up libhts2:s390x (1.7-2) ... Setting up libtabixpp0:s390x (1.0.0-3build2) ... Setting up libhts-dev:s390x (1.7-2) ... Setting up libpangocairo-1.0-0:s390x (1.40.14-1) ... Setting up samtools (1.7-1) ... Setting up libtabixpp-dev:s390x (1.0.0-3build2) ... Setting up r-base-core (3.4.4-1ubuntu1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-nnet (7.3-12-2build1) ... Setting up r-cran-spatial (7.3-11-2build1) ... Setting up r-cran-mass (7.3-49-1) ... Setting up r-cran-cluster (2.0.6-2build1) ... Setting up r-cran-boot (1.3-20-1.1) ... Setting up r-cran-codetools (0.2-15-1.1) ... Setting up r-cran-lattice (0.20-35-1build1) ... Setting up r-cran-nlme (3.1.131-3build1) ... Setting up r-cran-foreign (0.8.69-1build1) ... Setting up r-cran-class (7.3-14-2build1) ... Setting up r-cran-kernsmooth (2.23-15-3build1) ... Setting up r-cran-matrix (1.2-12-1) ... Setting up r-cran-mgcv (1.8-23-1) ... Setting up r-cran-survival (2.41-3-2build1) ... Setting up r-cran-rpart (4.1-13-1) ... Setting up r-recommended (3.4.4-1ubuntu1) ... Setting up r-base (3.4.4-1ubuntu1) ... Setting up dh-autoreconf (17) ... Setting up rake (12.3.1-1) ... Setting up dh-strip-nondeterminism (0.040-1.1~build1) ... Setting up debhelper (11.1.6ubuntu1) ... Setting up ruby2.5 (2.5.1-1ubuntu1) ... Setting up ruby (1:2.5.1) ... Setting up ruby-test-unit (3.2.5-1) ... Setting up asciidoctor (1.5.5-1) ... Setting up sbuild-build-depends-reapr-dummy (0.invalid.0) ... Setting up libruby2.5:s390x (2.5.1-1ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Processing triggers for systemd (237-3ubuntu10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-121-generic s390x (s390x) Toolchain package versions: binutils_2.30-15ubuntu1 dpkg-dev_1.19.0.5ubuntu2 g++-7_7.3.0-16ubuntu3 gcc-7_7.3.0-16ubuntu3 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-16ubuntu3 libstdc++6_8-20180414-1ubuntu2 linux-libc-dev_4.15.0-20.21 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.6.1 asciidoctor_1.5.5-1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6 autotools-dev_20180224.1 bamtools_2.4.1+dfsg-2 base-files_10.1ubuntu2 base-passwd_3.5.44 bash_4.4.18-2ubuntu1 binutils_2.30-15ubuntu1 binutils-common_2.30-15ubuntu1 binutils-s390x-linux-gnu_2.30-15ubuntu1 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.31.1-0.4ubuntu3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2 cpp-7_7.3.0-16ubuntu3 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.1.6ubuntu1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu2 dpkg-dev_1.19.0.5ubuntu2 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3 file_1:5.32-2 findutils_4.6.0+git+20170828-2 fontconfig_2.12.6-0ubuntu2 fontconfig-config_2.12.6-0ubuntu2 fonts-dejavu-core_2.37-1 g++_4:7.3.0-3ubuntu2 g++-7_7.3.0-16ubuntu3 gcc_4:7.3.0-3ubuntu2 gcc-7_7.3.0-16ubuntu3 gcc-7-base_7.3.0-16ubuntu3 gcc-8-base_8-20180414-1ubuntu2 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gpg_2.2.4-1ubuntu1 gpg-agent_2.2.4-1ubuntu1 gpgconf_2.2.4-1ubuntu1 gpgv_2.2.4-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 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libudev1_237-3ubuntu10 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.4ubuntu3 libwind0-heimdal_7.5.0+dfsg-1 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1 libxcb-render0_1.13-1 libxcb-shm0_1.13-1 libxcb1_1.13-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml2_2.9.4+dfsg1-6.1ubuntu1 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 libyaml-0-2_0.1.7-2ubuntu3 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-20.21 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mount_2.31.1-0.4ubuntu3 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1-1ubuntu1 ncurses-bin_6.1-1ubuntu1 openssl_1.1.0g-2ubuntu4 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.1-6 perl-base_5.26.1-6 perl-modules-5.26_5.26.1-6 pinentry-curses_1.1.0-1 pkgbinarymangler_138 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1 r-base_3.4.4-1ubuntu1 r-base-core_3.4.4-1ubuntu1 r-cran-boot_1.3-20-1.1 r-cran-class_7.3-14-2build1 r-cran-cluster_2.0.6-2build1 r-cran-codetools_0.2-15-1.1 r-cran-foreign_0.8.69-1build1 r-cran-kernsmooth_2.23-15-3build1 r-cran-lattice_0.20-35-1build1 r-cran-mass_7.3-49-1 r-cran-matrix_1.2-12-1 r-cran-mgcv_1.8-23-1 r-cran-nlme_3.1.131-3build1 r-cran-nnet_7.3-12-2build1 r-cran-rpart_4.1-13-1 r-cran-spatial_7.3-11-2build1 r-cran-survival_2.41-3-2build1 r-recommended_3.4.4-1ubuntu1 rake_12.3.1-1 readline-common_7.0-3 ruby_1:2.5.1 ruby-did-you-mean_1.2.0-2 ruby-minitest_5.10.3-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.3.0-1 ruby-test-unit_3.2.5-1 ruby2.5_2.5.1-1ubuntu1 rubygems-integration_1.11 samtools_1.7-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-reapr-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 smalt_0.7.6-7 snpomatic_1.0-3 systemd_237-3ubuntu10 systemd-sysv_237-3ubuntu10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tabix_1.7-2 tar_1.29b-2 tzdata_2018d-1 ubuntu-keyring_2018.02.28 ucf_3.0038 unzip_6.0-21ubuntu1 util-linux_2.31.1-0.4ubuntu3 x11-common_1:7.7+19ubuntu7 xdg-utils_1.1.2-1ubuntu2 xz-utils_5.2.2-1.3 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Jul 12 09:02:08 2016 UTC gpgv: using RSA key E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./reapr_1.0.18+dfsg-3.dsc dpkg-source: info: extracting reapr in reapr-1.0.18+dfsg dpkg-source: info: unpacking reapr_1.0.18+dfsg.orig.tar.gz dpkg-source: info: unpacking reapr_1.0.18+dfsg-3.debian.tar.xz dpkg-source: info: applying spelling dpkg-source: info: applying use_shared_libs dpkg-source: info: applying hardening dpkg-source: info: applying fix_sort_samtools13 dpkg-source: info: applying ld_as_needed Check disc 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-14622629 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14622629 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14622629 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package reapr dpkg-buildpackage: info: source version 1.0.18+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build reapr-1.0.18+dfsg dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' rm -rf /<>/reapr-1.0.18+dfsg/debian/man_src/*.html /<>/reapr-1.0.18+dfsg/debian/man_src/*.? rm -rf /<>/reapr-1.0.18+dfsg/debian/man rm -rf /<>/reapr-1.0.18+dfsg/debian/test dh_auto_clean -- make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' cd src && /usr/bin/make make[2]: Entering directory '/<>/reapr-1.0.18+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c histogram.cpp histogram.cpp: In member function ‘void Histogram::plot(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)’: histogram.cpp:333:50: warning: ‘stddev’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (plotTrim_ && xval < mean - plotTrim_ * stddev) ~~~~~~~~~~^~~~~~~~ histogram.cpp:321:17: warning: ‘mean’ may be used uninitialized in this function [-Wmaybe-uninitialized] mean = mean ? mean : 1; ~~~~~^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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] map > >::iterator p = globalGaps.find(currentRefID); ^ g++ -o task_score -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 ‘int main(int, char**)’: task_stats.cpp:441:16: warning: ‘ti_perfect’ may be used uninitialized in this function [-Wmaybe-uninitialized] delete ti_perfect; ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 between signed and unsigned integer expressions [-Wsign-compare] while (bamAlign.Position > triplot.centreCoord()) ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bam2fcdEstimate.cpp: In function ‘void initialiseFCDHists(std::vector&, CmdLineOptions&)’: bam2fcdEstimate.cpp:210:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (unsigned long i = 0; i <= ops.maxInsert; i++) ~~^~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 between signed and unsigned integer expressions [-Wsign-compare] if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) ~~~~~~~~~~~~~~~~^~~~~~~~~ task_gapresize.cpp:129:148: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] 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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 between signed and unsigned integer expressions [-Wsign-compare] if (p->second.Position >= endPos) break; ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -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 -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/<>/reapr-1.0.18+dfsg/src' make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' mkdir /<>/reapr-1.0.18+dfsg/debian/test ln -s /<>/reapr-1.0.18+dfsg/src/reapr.pl /<>/reapr-1.0.18+dfsg/debian/test/reapr PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/<>/reapr-1.0.18+dfsg/src:/<>/reapr-1.0.18+dfsg/debian/test /<>/reapr-1.0.18+dfsg/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.3924.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.3924.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.3924.smaltmap.smalt_sample out.bam.tmp.3924.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.3924.smaltmap.smalt_sample out.bam.tmp.3924.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:4 seconds # smalt: Total elapsed wall clock time: 4 seconds [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.3924.smaltmap.smalt_sample -f samsoft out.bam.tmp.3924.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.3924.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.3924.smaltmap.smalt_sample -f samsoft out.bam.tmp.3924.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:18 seconds # smalt: Total elapsed wall clock time: 18 seconds [REAPR smaltmap] Running: samtools sort out.bam.tmp.3924.smaltmap.raw.bam -O bam -o out.bam.tmp.3924.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.3924.smaltmap.raw.bam.sort.bam out.bam.tmp.3924.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.3924.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.3924.smaltmap.rmdup.bam >> out.bam.tmp.3924.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.3924.smaltmap.header out.bam.tmp.3924.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.3924.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck [REAPR pipeline] Running preprocess terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases [REAPR preprocess] No coverage in foo:1169-3476. Skipping [REAPR preprocess] sampling region foo:3492-5726. Already sampled 0 bases [REAPR preprocess] No coverage in foo:3492-5726. Skipping [REAPR preprocess] sampling region foo:5756-12551. Already sampled 0 bases [REAPR preprocess] No coverage in foo:5756-12551. Skipping [REAPR preprocess] sampling region foo:12591-998105. Already sampled 0 bases [REAPR preprocess] No coverage in foo:12591-998105. Skipping [REAPR preprocess] Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' Most likely causes are: 1. A character in the assembly sequence names that broke tabix, such as :,| or -. You can check for this by running reapr facheck 2. A mismatch of names in the input BAM and assembly fasta files. A common cause is trailing whitespace in the fasta file, or everything after the first whitesace character in a name being removed by the mapper, so the name is different in the BAM file. 3. There is not enough fragment coverage because the assembly is too fragmented. You may want to compare your mean contig length with the insert size of the reads. Also have a look at this plot of the insert size distribution: 00.Sample/insert.in.pdf debian/rules:33: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' debian/rules:4: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20180427-1117 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 34904 Build-Time: 70 Distribution: bionic Fail-Stage: build Host Architecture: s390x Install-Time: 22 Job: reapr_1.0.18+dfsg-3.dsc Machine Architecture: s390x Package: reapr Package-Time: 93 Source-Version: 1.0.18+dfsg-3 Space: 34904 Status: attempted Version: 1.0.18+dfsg-3 -------------------------------------------------------------------------------- Finished at 20180427-1117 Build needed 00:01:33, 34904k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=s390x PACKAGEBUILD-14622629 Scanning for processes to kill in build PACKAGEBUILD-14622629 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=s390x PACKAGEBUILD-14622629 Stopping target for build PACKAGEBUILD-14622629 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=s390x PACKAGEBUILD-14622629 Removing build PACKAGEBUILD-14622629