https://launchpad.net/ubuntu/+source/nanopolish/0.13.2-1build1/+build/19306245 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-022 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:06 UTC 2020 ppc64le Buildd toolchain package versions: launchpad-buildd_189 python-lpbuildd_189 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_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.9 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 21 May 15:03:31 ntpdate[1895]: adjust time server 10.211.37.1 offset 0.012179 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=ppc64el PACKAGEBUILD-19306245 --image-type chroot /home/buildd/filecache-default/2b938910cc1b05b915dfd011059e884e9b102147 Creating target for build PACKAGEBUILD-19306245 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=ppc64el PACKAGEBUILD-19306245 Starting target for build PACKAGEBUILD-19306245 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=ppc64el PACKAGEBUILD-19306245 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19306245 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=ppc64el PACKAGEBUILD-19306245 Updating target for build PACKAGEBUILD-19306245 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [268 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [119 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main ppc64el Packages [937 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [507 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe ppc64el Packages [8485 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5172 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el Packages [55.7 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [31.7 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el Packages [490 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [260 kB] Fetched 16.5 MB in 4s (4520 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils cpp-9 dash debconf e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv libacl1 libapparmor1 libapt-pkg6.0 libasan5 libatomic1 libbinutils libblkid1 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgomp1 libidn2-0 libitm1 libkmod2 liblsan0 libmount1 libncurses6 libncursesw6 libperl5.30 libprocps8 libquadmath0 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 linux-libc-dev logsave make mount ncurses-base ncurses-bin perl perl-base perl-modules-5.30 procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata util-linux 77 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 53.4 MB of archives. After this operation, 403 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main ppc64el libcrypt-dev ppc64el 1:4.4.15-1ubuntu1 [139 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main ppc64el libcrypt1 ppc64el 1:4.4.15-1ubuntu1 [105 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main ppc64el base-files ppc64el 11ubuntu7 [60.3 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el bsdutils ppc64el 1:2.35.1-5ubuntu2 [91.8 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el perl-modules-5.30 all 5.30.2-1 [2740 kB] Get:6 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libperl5.30 ppc64el 5.30.2-1 [3907 kB] Get:7 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el perl ppc64el 5.30.2-1 [224 kB] Get:8 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el perl-base ppc64el 5.30.2-1 [1496 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main ppc64el debconf all 1.5.74 [121 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main ppc64el dash ppc64el 0.5.10.2-7 [100 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main ppc64el ncurses-bin ppc64el 6.2-1 [180 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libblkid1 ppc64el 2.35.1-5ubuntu2 [153 kB] Get:13 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libuuid1 ppc64el 2.35.1-5ubuntu2 [23.5 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libfdisk1 ppc64el 2.35.1-5ubuntu2 [189 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libmount1 ppc64el 2.35.1-5ubuntu2 [166 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main ppc64el libncurses6 ppc64el 6.2-1 [120 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main ppc64el libncursesw6 ppc64el 6.2-1 [152 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main ppc64el libtinfo6 ppc64el 6.2-1 [102 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libsmartcols1 ppc64el 2.35.1-5ubuntu2 [107 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el fdisk ppc64el 2.35.1-5ubuntu2 [132 kB] Get:21 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el util-linux ppc64el 2.35.1-5ubuntu2 [1093 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main ppc64el ncurses-base all 6.2-1 [18.7 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main ppc64el sysvinit-utils ppc64el 2.96-3ubuntu1 [22.8 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main ppc64el libatomic1 ppc64el 10.1.0-2ubuntu1 [9992 B] Get:25 http://ftpmaster.internal/ubuntu groovy/main ppc64el libubsan1 ppc64el 10.1.0-2ubuntu1 [149 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main ppc64el libtsan0 ppc64el 10.1.0-2ubuntu1 [326 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main ppc64el libquadmath0 ppc64el 10.1.0-2ubuntu1 [153 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main ppc64el liblsan0 ppc64el 10.1.0-2ubuntu1 [156 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main ppc64el libitm1 ppc64el 10.1.0-2ubuntu1 [28.5 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main ppc64el libgomp1 ppc64el 10.1.0-2ubuntu1 [108 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main ppc64el gcc-10-base ppc64el 10.1.0-2ubuntu1 [20.2 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main ppc64el libgcc-s1 ppc64el 10.1.0-2ubuntu1 [30.3 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main ppc64el libcc1-0 ppc64el 10.1.0-2ubuntu1 [41.9 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main ppc64el libstdc++6 ppc64el 10.1.0-2ubuntu1 [546 kB] Get:35 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el systemd-sysv ppc64el 245.5-3ubuntu1 [10.3 kB] Get:36 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el systemd-timesyncd ppc64el 245.5-3ubuntu1 [28.6 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main ppc64el libacl1 ppc64el 2.2.53-8 [20.5 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main ppc64el libapparmor1 ppc64el 2.13.3-7ubuntu6 [38.1 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main ppc64el libcap2 ppc64el 1:2.34-2 [17.8 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main ppc64el libcryptsetup12 ppc64el 2:2.3.1-1ubuntu1 [226 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main ppc64el libidn2-0 ppc64el 2.3.0-1 [55.8 kB] Get:42 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libkmod2 ppc64el 27+20200310-2ubuntu1 [51.6 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main ppc64el libseccomp2 ppc64el 2.4.3-1ubuntu2 [47.1 kB] Get:44 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el mount ppc64el 2.35.1-5ubuntu2 [126 kB] Get:45 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el systemd ppc64el 245.5-3ubuntu1 [4589 kB] Get:46 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libsystemd0 ppc64el 245.5-3ubuntu1 [307 kB] Get:47 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libudev1 ppc64el 245.5-3ubuntu1 [88.1 kB] Get:48 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libapt-pkg6.0 ppc64el 2.1.4 [905 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main ppc64el gpgv ppc64el 2.2.20-1ubuntu1 [232 kB] Get:50 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el apt ppc64el 2.1.4 [1317 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main ppc64el logsave ppc64el 1.45.6-1ubuntu1 [10.8 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main ppc64el libext2fs2 ppc64el 1.45.6-1ubuntu1 [215 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main ppc64el e2fsprogs ppc64el 1.45.6-1ubuntu1 [557 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main ppc64el libcom-err2 ppc64el 1.45.6-1ubuntu1 [10.1 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main ppc64el libprocps8 ppc64el 2:3.3.16-4ubuntu1 [35.9 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main ppc64el libss2 ppc64el 1.45.6-1ubuntu1 [12.4 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main ppc64el procps ppc64el 2:3.3.16-4ubuntu1 [250 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main ppc64el libsqlite3-0 ppc64el 3.31.1-5 [577 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main ppc64el tzdata all 2020a-0ubuntu1 [293 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main ppc64el libctf0 ppc64el 2.34-7ubuntu1 [52.8 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.34-7ubuntu1 [1747 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main ppc64el libbinutils ppc64el 2.34-7ubuntu1 [514 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main ppc64el binutils ppc64el 2.34-7ubuntu1 [3368 B] Get:64 http://ftpmaster.internal/ubuntu groovy/main ppc64el binutils-common ppc64el 2.34-7ubuntu1 [207 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main ppc64el libctf-nobfd0 ppc64el 2.34-7ubuntu1 [53.5 kB] Get:66 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libasan5 ppc64el 9.3.0-13ubuntu1 [408 kB] Get:67 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el g++-9 ppc64el 9.3.0-13ubuntu1 [7751 kB] Get:68 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el gcc-9 ppc64el 9.3.0-13ubuntu1 [7557 kB] Get:69 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libstdc++-9-dev ppc64el 9.3.0-13ubuntu1 [1752 kB] Get:70 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libgcc-9-dev ppc64el 9.3.0-13ubuntu1 [1260 kB] Get:71 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el cpp-9 ppc64el 9.3.0-13ubuntu1 [6835 kB] Get:72 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el gcc-9-base ppc64el 9.3.0-13ubuntu1 [19.7 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main ppc64el gpg ppc64el 2.2.20-1ubuntu1 [539 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main ppc64el gpgconf ppc64el 2.2.20-1ubuntu1 [143 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main ppc64el gpg-agent ppc64el 2.2.20-1ubuntu1 [267 kB] Get:76 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el linux-libc-dev ppc64el 5.4.0-29.33 [1093 kB] Get:77 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el make ppc64el 4.3-1 [178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.4 MB in 2s (34.2 MB/s) (Reading database ... 12761 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.15-1ubuntu1_ppc64el.deb ... Unpacking libcrypt-dev:ppc64el (1:4.4.15-1ubuntu1) over (1:4.4.10-10ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.15-1ubuntu1_ppc64el.deb ... Unpacking libcrypt1:ppc64el (1:4.4.15-1ubuntu1) over (1:4.4.10-10ubuntu4) ... Setting up libcrypt1:ppc64el (1:4.4.15-1ubuntu1) ... (Reading database ... 12761 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu7_ppc64el.deb ... Unpacking base-files (11ubuntu7) over (11ubuntu5) ... Setting up base-files (11ubuntu7) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/50-motd-news ... (Reading database ... 12761 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.35.1-5ubuntu2_ppc64el.deb ... 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Processing triggers for libc-bin (2.31-0ubuntu9) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19306245 ppc64el groovy-proposed -c chroot:build-PACKAGEBUILD-19306245 --arch=ppc64el --dist=groovy-proposed --nolog nanopolish_0.13.2-1build1.dsc Initiating build PACKAGEBUILD-19306245 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:06 UTC 2020 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-ppc64el-022.buildd +==============================================================================+ | nanopolish 0.13.2-1build1 (ppc64el) 21 May 2020 15:03 | +==============================================================================+ Package: nanopolish Version: 0.13.2-1build1 Source Version: 0.13.2-1build1 Distribution: groovy-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/nanopolish-SAg44I/nanopolish-0.13.2' with '<>' I: NOTICE: Log filtering will replace 'build/nanopolish-SAg44I' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19306245/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- nanopolish_0.13.2-1build1.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-cAfImz/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-cAfImz/apt_archive ./ InRelease Get:2 copy:/<>/resolver-cAfImz/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-cAfImz/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-cAfImz/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-cAfImz/apt_archive ./ Packages [529 B] Fetched 2862 B in 0s (176 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-cAfImz/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12769 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev Filtered Build-Depends: debhelper-compat (= 12), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev dpkg-deb: building package 'sbuild-build-depends-nanopolish-dummy' in '/<>/resolver-QOQZGu/apt_archive/sbuild-build-depends-nanopolish-dummy.deb'. Ign:1 copy:/<>/resolver-QOQZGu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-QOQZGu/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-QOQZGu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-QOQZGu/apt_archive ./ Sources [271 B] Get:5 copy:/<>/resolver-QOQZGu/apt_archive ./ Packages [593 B] Fetched 2983 B in 0s (184 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install nanopolish build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libeigen3-dev libelf1 libexpat1 libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libminimap2-dev libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libsz2 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libeigen3-doc libmpfrc++-dev krb5-doc krb5-user libhdf5-doc liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support 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 The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbsd0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libeigen3-dev libelf1 libexpat1 libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libminimap2-dev libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libsz2 libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-minimal sbuild-build-depends-nanopolish-dummy zlib1g-dev 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 33.3 MB of archives. After this operation, 152 MB of additional disk space will be used. 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3.8.2-0ubuntu2 [7068 B] Get:11 http://ftpmaster.internal/ubuntu groovy/main ppc64el python3 ppc64el 3.8.2-0ubuntu2 [47.6 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main ppc64el libbsd0 ppc64el 0.10.0-1 [55.1 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main ppc64el bsdmainutils ppc64el 11.1.2ubuntu3 [187 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main ppc64el libuchardet0 ppc64el 0.0.6-3build1 [67.9 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main ppc64el groff-base ppc64el 1.22.4-5 [922 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main ppc64el libpipeline1 ppc64el 1.5.2-2build1 [28.9 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main ppc64el man-db ppc64el 2.9.1-1 [1143 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libmagic-mgc ppc64el 1:5.38-5 [218 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el libmagic1 ppc64el 1:5.38-5 [93.2 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el file ppc64el 1:5.38-5 [24.2 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main ppc64el libelf1 ppc64el 0.176-1.1build1 [53.4 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main ppc64el libglib2.0-0 ppc64el 2.64.2-1 [1381 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main ppc64el libicu66 ppc64el 66.1-2ubuntu2 [8595 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main ppc64el libxml2 ppc64el 2.9.10+dfsg-5 [671 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main ppc64el gettext-base ppc64el 0.19.8.1-10build1 [52.5 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main ppc64el libkrb5support0 ppc64el 1.17-6ubuntu4 [34.9 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main ppc64el libk5crypto3 ppc64el 1.17-6ubuntu4 [102 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main ppc64el libkeyutils1 ppc64el 1.6.1-2ubuntu1 [11.3 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main ppc64el libkrb5-3 ppc64el 1.17-6ubuntu4 [371 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main ppc64el libgssapi-krb5-2 ppc64el 1.17-6ubuntu4 [135 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main ppc64el libpsl5 ppc64el 0.21.0-1ubuntu1 [53.2 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main ppc64el libsigsegv2 ppc64el 2.12-2 [13.9 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main ppc64el m4 ppc64el 1.4.18-4 [210 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main ppc64el autoconf all 2.69-11.1 [321 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main ppc64el autotools-dev all 20180224.1 [39.6 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main ppc64el automake all 1:1.16.1-4ubuntu6 [522 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main ppc64el autopoint all 0.19.8.1-10build1 [412 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main ppc64el libtool all 2.4.6-14 [161 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main ppc64el dh-autoreconf all 19 [16.1 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main ppc64el libdebhelper-perl all 13ubuntu1 [62.5 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main ppc64el libsub-override-perl all 0.09-2 [9532 B] Get:43 http://ftpmaster.internal/ubuntu groovy/main ppc64el libfile-stripnondeterminism-perl all 1.8.0-1 [16.2 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main ppc64el dh-strip-nondeterminism all 1.8.0-1 [5228 B] Get:45 http://ftpmaster.internal/ubuntu groovy/main ppc64el dwz ppc64el 0.13-5 [136 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main ppc64el libcroco3 ppc64el 0.6.13-1 [92.1 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main ppc64el gettext ppc64el 0.19.8.1-10build1 [959 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main ppc64el po-debconf all 1.0.21 [233 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main ppc64el debhelper all 13ubuntu1 [877 kB] Get:51 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el python3-lib2to3 all 3.8.3-2 [74.1 kB] Get:52 http://ftpmaster.internal/ubuntu groovy-proposed/main ppc64el python3-distutils all 3.8.3-2 [140 kB] Get:53 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el dh-python all 4.20200315 [85.8 kB] Get:54 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el hdf5-helpers ppc64el 1.10.6+repack-2 [13.7 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/universe ppc64el libaec0 ppc64el 1.0.4-1 [24.4 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main ppc64el libroken18-heimdal ppc64el 7.7.0+dfsg-2 [46.4 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main ppc64el libasn1-8-heimdal ppc64el 7.7.0+dfsg-2 [176 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main ppc64el libbrotli1 ppc64el 1.0.7-6.1 [293 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main ppc64el libheimbase1-heimdal ppc64el 7.7.0+dfsg-2 [32.4 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main ppc64el libhcrypto4-heimdal ppc64el 7.7.0+dfsg-2 [108 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main ppc64el libwind0-heimdal ppc64el 7.7.0+dfsg-2 [48.9 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main ppc64el libhx509-5-heimdal ppc64el 7.7.0+dfsg-2 [120 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main ppc64el libkrb5-26-heimdal ppc64el 7.7.0+dfsg-2 [234 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main ppc64el libheimntlm0-heimdal ppc64el 7.7.0+dfsg-2 [17.4 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main ppc64el libgssapi3-heimdal ppc64el 7.7.0+dfsg-2 [105 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main ppc64el libsasl2-modules-db ppc64el 2.1.27+dfsg-2 [16.9 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main ppc64el libsasl2-2 ppc64el 2.1.27+dfsg-2 [60.2 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main ppc64el libldap-common all 2.4.49+dfsg-2ubuntu2 [17.4 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main ppc64el libldap-2.4-2 ppc64el 2.4.49+dfsg-2ubuntu2 [176 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main ppc64el libnghttp2-14 ppc64el 1.40.0-1build1 [91.3 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build1 [59.3 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main ppc64el libssh-4 ppc64el 0.9.4-1ubuntu1 [195 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main ppc64el libcurl3-gnutls ppc64el 7.68.0-1ubuntu2 [254 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/universe ppc64el libdeflate0 ppc64el 1.6-1 [64.0 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/universe ppc64el libsz2 ppc64el 1.0.4-1 [5416 B] Get:76 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el libhdf5-103-1 ppc64el 1.10.6+repack-2 [1120 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main ppc64el libgfortran5 ppc64el 10.1.0-2ubuntu1 [689 kB] Get:78 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el libhdf5-fortran-102 ppc64el 1.10.6+repack-2 [82.3 kB] Get:79 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el libhdf5-hl-100 ppc64el 1.10.6+repack-2 [63.6 kB] Get:80 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el libhdf5-hl-fortran-100 ppc64el 1.10.6+repack-2 [30.1 kB] Get:81 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el libhdf5-cpp-103-1 ppc64el 1.10.6+repack-2 [112 kB] Get:82 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el libhdf5-hl-cpp-100 ppc64el 1.10.6+repack-2 [10.1 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-2ubuntu1 [165 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main ppc64el libjpeg-turbo8 ppc64el 2.0.3-0ubuntu1 [155 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/main ppc64el libjpeg-turbo8-dev ppc64el 2.0.3-0ubuntu1 [276 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main ppc64el libjpeg8 ppc64el 8c-2ubuntu8 [2146 B] Get:87 http://ftpmaster.internal/ubuntu groovy/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu8 [1606 B] Get:88 http://ftpmaster.internal/ubuntu groovy/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu8 [1602 B] Get:89 http://ftpmaster.internal/ubuntu groovy/universe ppc64el libaec-dev ppc64el 1.0.4-1 [56.6 kB] Get:90 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el libhdf5-dev ppc64el 1.10.6+repack-2 [2731 kB] Get:91 http://ftpmaster.internal/ubuntu groovy-proposed/universe ppc64el libfast5-dev all 0.6.5-4build2 [49.1 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/universe ppc64el libhts3 ppc64el 1.10.2-3 [397 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main ppc64el liblzma-dev ppc64el 5.2.4-1 [166 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/universe ppc64el libhts-dev ppc64el 1.10.2-3 [92.0 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/universe ppc64el libminimap2-dev ppc64el 2.17+dfsg-9 [118 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main ppc64el pkg-config ppc64el 0.29.2-1ubuntu1 [49.5 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/universe ppc64el libeigen3-dev all 3.3.7-2 [815 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.3 MB in 2s (16.4 MB/s) Selecting previously unselected package libpython3.8-minimal:ppc64el. (Reading database ... 12769 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.3-1_ppc64el.deb ... Unpacking libpython3.8-minimal:ppc64el (3.8.3-1) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../libexpat1_2.2.9-1build1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.3-1_ppc64el.deb ... Unpacking python3.8-minimal (3.8.3-1) ... Setting up libpython3.8-minimal:ppc64el (3.8.3-1) ... Setting up libexpat1:ppc64el (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13060 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_ppc64el.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... Selecting previously unselected package mime-support. 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Preparing to unpack .../00-python3_3.8.2-0ubuntu2_ppc64el.deb ... Unpacking python3 (3.8.2-0ubuntu2) ... Selecting previously unselected package libbsd0:ppc64el. Preparing to unpack .../01-libbsd0_0.10.0-1_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_11.1.2ubuntu3_ppc64el.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../03-libuchardet0_0.0.6-3build1_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.6-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../04-groff-base_1.22.4-5_ppc64el.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../05-libpipeline1_1.5.2-2build1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.2-2build1) ... Selecting previously unselected package man-db. 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Selecting previously unselected package libaec-dev:ppc64el. Preparing to unpack .../78-libaec-dev_1.0.4-1_ppc64el.deb ... Unpacking libaec-dev:ppc64el (1.0.4-1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../79-libhdf5-dev_1.10.6+repack-2_ppc64el.deb ... Unpacking libhdf5-dev (1.10.6+repack-2) ... Selecting previously unselected package libfast5-dev. Preparing to unpack .../80-libfast5-dev_0.6.5-4build2_all.deb ... Unpacking libfast5-dev (0.6.5-4build2) ... Selecting previously unselected package libhts3:ppc64el. Preparing to unpack .../81-libhts3_1.10.2-3_ppc64el.deb ... Unpacking libhts3:ppc64el (1.10.2-3) ... Selecting previously unselected package liblzma-dev:ppc64el. Preparing to unpack .../82-liblzma-dev_5.2.4-1_ppc64el.deb ... Unpacking liblzma-dev:ppc64el (5.2.4-1) ... Selecting previously unselected package libhts-dev:ppc64el. Preparing to unpack .../83-libhts-dev_1.10.2-3_ppc64el.deb ... Unpacking libhts-dev:ppc64el (1.10.2-3) ... 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Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:ppc64el (2.64.2-1) ... No schema files found: doing nothing. Setting up libicu66:ppc64el (66.1-2ubuntu2) ... Setting up libdebhelper-perl (13ubuntu1) ... Setting up libbrotli1:ppc64el (1.0.7-6.1) ... Setting up libnghttp2-14:ppc64el (1.40.0-1build1) ... Setting up libmagic1:ppc64el (1:5.38-5) ... Setting up libdeflate0:ppc64el (1.6-1) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu2) ... Setting up libaec0:ppc64el (1.0.4-1) ... Setting up libkrb5support0:ppc64el (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:ppc64el (2.1.27+dfsg-2) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libsigsegv2:ppc64el (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up libk5crypto3:ppc64el (1.17-6ubuntu4) ... Setting up libjpeg-turbo8:ppc64el (2.0.3-0ubuntu1) ... Setting up libsasl2-2:ppc64el (2.1.27+dfsg-2) ... Setting up libgfortran5:ppc64el (10.1.0-2ubuntu1) ... Setting up libroken18-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up liblzma-dev:ppc64el (5.2.4-1) ... Setting up zlib1g-dev:ppc64el (1:1.2.11.dfsg-2ubuntu1) ... Setting up libuchardet0:ppc64el (0.0.6-3build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:ppc64el (1.17-6ubuntu4) ... Setting up libmpdec2:ppc64el (2.4.2-3) ... Setting up libpython3.8-stdlib:ppc64el (3.8.3-1) ... Setting up python3.8 (3.8.3-1) ... Setting up libbsd0:ppc64el (0.10.0-1) ... Setting up libelf1:ppc64el (0.176-1.1build1) ... Setting up libxml2:ppc64el (2.9.10+dfsg-5) ... Setting up libsz2:ppc64el (1.0.4-1) ... Setting up libpython3-stdlib:ppc64el (3.8.2-0ubuntu2) ... Setting up libheimbase1-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libjpeg8:ppc64el (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up libjpeg-turbo8-dev:ppc64el (2.0.3-0ubuntu1) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libaec-dev:ppc64el (1.0.4-1) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.2-0ubuntu2) ... Setting up libhcrypto4-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libwind0-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libminimap2-dev (2.17+dfsg-9) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libeigen3-dev (3.3.7-2) ... Setting up libgssapi-krb5-2:ppc64el (1.17-6ubuntu4) ... Setting up libcroco3:ppc64el (0.6.13-1) ... Setting up libssh-4:ppc64el (0.9.4-1ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up libhdf5-103-1:ppc64el (1.10.6+repack-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libhdf5-cpp-103-1:ppc64el (1.10.6+repack-2) ... Setting up libjpeg8-dev:ppc64el (8c-2ubuntu8) ... Setting up python3-lib2to3 (3.8.3-2) ... Setting up libhdf5-hl-100:ppc64el (1.10.6+repack-2) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.3-2) ... Setting up dh-python (4.20200315) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libhx509-5-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libjpeg-dev:ppc64el (8c-2ubuntu8) ... Setting up man-db (2.9.1-1) ... 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 intltool-debian (0.35.0+20060710.5) ... Setting up libhdf5-hl-cpp-100:ppc64el (1.10.6+repack-2) ... Setting up libhdf5-fortran-102:ppc64el (1.10.6+repack-2) ... Setting up libhdf5-hl-fortran-100:ppc64el (1.10.6+repack-2) ... Setting up libkrb5-26-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:ppc64el (7.7.0+dfsg-2) ... Setting up libhdf5-dev (1.10.6+repack-2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/powerpc64le-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libldap-2.4-2:ppc64el (2.4.49+dfsg-2ubuntu2) ... Setting up libcurl3-gnutls:ppc64el (7.68.0-1ubuntu2) ... Setting up libfast5-dev (0.6.5-4build2) ... Setting up libhts3:ppc64el (1.10.2-3) ... Setting up libhts-dev:ppc64el (1.10.2-3) ... Setting up debhelper (13ubuntu1) ... Setting up sbuild-build-depends-nanopolish-dummy (0.invalid.0) ... Setting up dh-autoreconf (19) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-179-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-13ubuntu1 gcc-9_9.3.0-13ubuntu1 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-2ubuntu1 linux-libc-dev_5.4.0-29.33 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.4 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-7ubuntu1 binutils-common_2.34-7ubuntu1 binutils-powerpc64le-linux-gnu_2.34-7ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.35.1-5ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-13ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20200315 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fdisk_2.35.1-5ubuntu2 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-13ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-2ubuntu1 gcc-9_9.3.0-13ubuntu1 gcc-9-base_9.3.0-13ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-0ubuntu4 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-13ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7ubuntu2 libatomic1_10.1.0-2ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-7ubuntu1 libblkid1_2.35.1-5ubuntu2 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.31-0ubuntu9 libc-dev-bin_2.31-0ubuntu9 libc6_2.31-0ubuntu9 libc6-dev_2.31-0ubuntu9 libcap-ng0_0.7.9-2.1build1 libcap2_1:2.34-2 libcc1-0_10.1.0-2ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.15-1ubuntu1 libcrypt1_1:4.4.15-1ubuntu1 libcryptsetup12_2:2.3.1-1ubuntu1 libctf-nobfd0_2.34-7ubuntu1 libctf0_2.34-7ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu2 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_13ubuntu1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu1 libdpkg-perl_1.19.7ubuntu3 libeigen3-dev_3.3.7-2 libelf1_0.176-1.1build1 libexpat1_2.2.9-1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libfast5-dev_0.6.5-4build2 libfdisk1_2.35.1-5ubuntu2 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgcc-9-dev_9.3.0-13ubuntu1 libgcc-s1_10.1.0-2ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10.1.0-2ubuntu1 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2ubuntu1 libgomp1_10.1.0-2ubuntu1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-6ubuntu4 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libhx509-5-heimdal_7.7.0+dfsg-2 libicu66_66.1-2ubuntu2 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libitm1_10.1.0-2ubuntu1 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_2.0.3-0ubuntu1 libjpeg-turbo8-dev_2.0.3-0ubuntu1 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libjson-c4_0.13.1+dfsg-7 libk5crypto3_1.17-6ubuntu4 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-6ubuntu4 libkrb5support0_1.17-6ubuntu4 libldap-2.4-2_2.4.49+dfsg-2ubuntu2 libldap-common_2.4.49+dfsg-2ubuntu2 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.1.0-2ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libminimap2-dev_2.17+dfsg-9 libmount1_2.35.1-5ubuntu2 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1build1 libnpth0_1.6-1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.2-1 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-4ubuntu1 libpsl5_0.21.0-1ubuntu1 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8-minimal_3.8.3-1 libpython3.8-stdlib_3.8.3-1 libquadmath0_10.1.0-2ubuntu1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1ubuntu2 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5ubuntu2 libsqlite3-0_3.31.1-5 libss2_1.45.6-1ubuntu1 libssh-4_0.9.4-1ubuntu1 libssl1.1_1.1.1f-1ubuntu2 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-2ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.5-3ubuntu1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10.1.0-2ubuntu1 libubsan1_10.1.0-2ubuntu1 libuchardet0_0.0.6-3build1 libudev1_245.5-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.35.1-5ubuntu2 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-29.33 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu5 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-1 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.35.1-5ubuntu2 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1f-1ubuntu2 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu5 patch_2.7.6-6 perl_5.30.2-1 perl-base_5.30.2-1 perl-modules-5.30_5.30.2-1 pinentry-curses_1.1.0-3build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-4ubuntu1 python3_3.8.2-0ubuntu2 python3-distutils_3.8.3-2 python3-lib2to3_3.8.3-2 python3-minimal_3.8.2-0ubuntu2 python3.8_3.8.3-1 python3.8-minimal_3.8.3-1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-nanopolish-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_245.5-3ubuntu1 systemd-sysv_245.5-3ubuntu1 systemd-timesyncd_245.5-3ubuntu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.02.11.2 util-linux_2.35.1-5ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri May 15 10:17:51 2020 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./nanopolish_0.13.2-1build1.dsc dpkg-source: info: extracting nanopolish in nanopolish-0.13.2 dpkg-source: info: unpacking nanopolish_0.13.2.orig.tar.gz dpkg-source: info: unpacking nanopolish_0.13.2-1build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add-shebang-to-script.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying fix_remaining_python_interpreters.patch dpkg-source: info: applying staticMinimap2Library.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19306245 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19306245 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19306245 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package nanopolish dpkg-buildpackage: info: source version 0.13.2-1build1 dpkg-buildpackage: info: source distribution groovy dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' sed -i~ 's/^.depend: .*/.depend:/' Makefile touch .depend /usr/bin/make clean make[2]: Entering directory '/<>' rm -f nanopolish nanopolish_test src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o \ src/main/nanopolish.o src/test/nanopolish_test.o make[2]: Leaving directory '/<>' rm -f .depend mv Makefile~ Makefile make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' rm -f ./.depend g++ -o src/main/nanopolish.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/main/nanopolish.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_extract.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend; g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_alignment_db.cpp g++ -o src/alignment/nanopolish_anchor.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_anchor.cpp g++ -o src/alignment/nanopolish_eventalign.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_eventalign.cpp g++ -o src/common/fs_support.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/fs_support.cpp g++ -o src/common/logsum.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/logsum.cpp g++ -o src/common/nanopolish_alphabet.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_alphabet.cpp g++ -o src/common/nanopolish_bam_processor.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_bam_processor.cpp g++ -o src/common/nanopolish_bam_utils.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_bam_utils.cpp g++ -o src/common/nanopolish_common.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_common.cpp g++ -o src/common/nanopolish_iupac.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_iupac.cpp g++ -o src/common/nanopolish_klcs.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_klcs.cpp g++ -o src/common/nanopolish_variant.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_variant.cpp g++ -o src/hmm/nanopolish_duration_model.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_duration_model.cpp g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm.cpp g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_transition_parameters.cpp g++ -o src/io/nanopolish_fast5_io.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_io.cpp g++ -o src/io/nanopolish_fast5_loader.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_loader.cpp g++ -o src/io/nanopolish_fast5_processor.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_processor.cpp g++ -o src/nanopolish_call_methylation.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_call_methylation.cpp g++ -o src/nanopolish_call_variants.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_call_variants.cpp g++ -o src/nanopolish_extract.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_extract.cpp src/nanopolish_call_methylation.cpp: In member function ‘void WatchStatus::update(const string&)’: src/nanopolish_call_methylation.cpp:120:73: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘double’ [-Wformat=] 120 | fprintf(stderr, "\33[2K\r[call-methylation] fast5 progress: %d/%d %.2lfs/fast5 [%s]", processed_fast5s, seconds_per_file, total_fast5s, message.c_str()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int double | %f src/nanopolish_call_methylation.cpp:120:79: warning: format ‘%lf’ expects argument of type ‘double’, but argument 5 has type ‘int’ [-Wformat=] 120 | fprintf(stderr, "\33[2K\r[call-methylation] fast5 progress: %d/%d %.2lfs/fast5 [%s]", processed_fast5s, seconds_per_file, total_fast5s, message.c_str()); | ~~~~^ ~~~~~~~~~~~~ | | | | double int | %.2d g++ -o src/nanopolish_getmodel.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_getmodel.cpp g++ -o src/nanopolish_haplotype.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_haplotype.cpp g++ -o src/nanopolish_index.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_index.cpp g++ -o src/nanopolish_methyltrain.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_methyltrain.cpp g++ -o src/nanopolish_phase_reads.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_phase_reads.cpp g++ -o src/nanopolish_polya_estimator.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_polya_estimator.cpp src/nanopolish_phase_reads.cpp: In function ‘void phase_single_read(const ReadDB&, const faidx_t*, const std::vector&, samFile*, const bam_hdr_t*, const bam1_t*, size_t, int, int)’: src/nanopolish_phase_reads.cpp:313:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 313 | fprintf(stderr, "warning: reference base at position %d does not match variant record (%c != %c)\n", | ~^ | | | int | %ld 314 | v.ref_position, v.ref_seq[0], read_outseq[out_position]); | ~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} src/nanopolish_polya_estimator.cpp: In function ‘void estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)’: src/nanopolish_polya_estimator.cpp:781:70: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘uint32_t’ {aka ‘unsigned int’} [-Wformat=] 781 | fprintf(stderr, "[polya] read: %s length: %zu prefix clip: %zu suffix clip %zu\n", | ~~^ | | | long unsigned int | %u 782 | read_name.c_str(), sr.read_sequence.length(), prefix_clip, suffix_clip); | ~~~~~~~~~~~ | | | uint32_t {aka unsigned int} src/nanopolish_polya_estimator.cpp:781:86: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 6 has type ‘uint32_t’ {aka ‘unsigned int’} [-Wformat=] 781 | fprintf(stderr, "[polya] read: %s length: %zu prefix clip: %zu suffix clip %zu\n", | ~~^ | | | long unsigned int | %u 782 | read_name.c_str(), sr.read_sequence.length(), prefix_clip, suffix_clip); | ~~~~~~~~~~~ | | | uint32_t {aka unsigned int} g++ -o src/nanopolish_raw_loader.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_raw_loader.cpp g++ -o src/nanopolish_read_db.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_read_db.cpp g++ -o src/nanopolish_scorereads.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_scorereads.cpp g++ -o src/nanopolish_squiggle_read.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_squiggle_read.cpp g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp g++ -o src/nanopolish_variant_db.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_variant_db.cpp g++ -o src/nanopolish_vcf2fasta.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_vcf2fasta.cpp g++ -o src/pore_model/nanopolish_model_names.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_model_names.cpp g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_pore_model_set.cpp g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_poremodel.cpp g++ -o src/training_core.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/training_core.cpp cc -o src/thirdparty/fet.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/fet.c cc -o src/thirdparty/scrappie/event_detection.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/scrappie/event_detection.c cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/scrappie/scrappie_common.c cc -o src/thirdparty/stdaln.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/stdaln.c g++ -o nanopolish -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib/powerpc64le-linux-gnu/hdf5/serial make[1]: Leaving directory '/<>' dh_auto_test -a make -j4 test make[1]: Entering directory '/<>' g++ -o src/test/nanopolish_test.o -c -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/test/nanopolish_test.cpp In file included from /usr/include/powerpc64le-linux-gnu/asm/sigcontext.h:12, from /usr/include/powerpc64le-linux-gnu/bits/sigcontext.h:30, from /usr/include/signal.h:291, from src/test/catch.hpp:5155, from src/test/nanopolish_test.cpp:16: ./src/nanopolish_squiggle_read.h:25:5: error: expected identifier before numeric constant 25 | PT_R7, | ^~~~~ ./src/nanopolish_squiggle_read.h:25:5: error: expected ‘}’ before numeric constant In file included from ./src/hmm/nanopolish_emissions.h:14, from src/test/nanopolish_test.cpp:19: ./src/nanopolish_squiggle_read.h:23:1: note: to match this ‘{’ 23 | { | ^ In file included from /usr/include/powerpc64le-linux-gnu/asm/sigcontext.h:12, from /usr/include/powerpc64le-linux-gnu/bits/sigcontext.h:30, from /usr/include/signal.h:291, from src/test/catch.hpp:5155, from src/test/nanopolish_test.cpp:16: ./src/nanopolish_squiggle_read.h:25:5: error: expected unqualified-id before numeric constant 25 | PT_R7, | ^~~~~ In file included from ./src/hmm/nanopolish_emissions.h:14, from src/test/nanopolish_test.cpp:19: ./src/nanopolish_squiggle_read.h:27:1: error: expected declaration before ‘}’ token 27 | }; | ^ make[1]: *** [Makefile:158: src/test/nanopolish_test.o] Error 1 make[1]: Leaving directory '/<>' dh_auto_test: error: make -j4 test returned exit code 2 make: *** [debian/rules:26: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200521-1505 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 118784 Build-Time: 99 Distribution: groovy-proposed Fail-Stage: build Host Architecture: ppc64el Install-Time: 16 Job: nanopolish_0.13.2-1build1.dsc Machine Architecture: ppc64el Package: nanopolish Package-Time: 116 Source-Version: 0.13.2-1build1 Space: 118784 Status: attempted Version: 0.13.2-1build1 -------------------------------------------------------------------------------- Finished at 20200521-1505 Build needed 00:01:56, 118784k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=ppc64el PACKAGEBUILD-19306245 Scanning for processes to kill in build PACKAGEBUILD-19306245