https://launchpad.net/ubuntu/+source/nanopolish/0.14.0-1ubuntu1/+build/25524220 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-029 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_228~614~ubuntu20.04.1 python3-lpbuildd_228~614~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.8 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 26 Jan 17:31:42 ntpdate[1845]: adjust time server 10.131.248.1 offset 0.000238 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25524220 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3 Creating target for build PACKAGEBUILD-25524220 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25524220 Starting target for build PACKAGEBUILD-25524220 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25524220 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-25524220 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25524220 Updating target for build PACKAGEBUILD-25524220 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 Packages [1385 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe amd64 Packages [14.4 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5890 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 Packages [199 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [67.0 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 Packages [925 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [382 kB] Fetched 24.3 MB in 3s (8887 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: adduser advancecomp apt bash binutils binutils-common binutils-x86-64-linux-gnu coreutils cpp-12 debconf diffutils dpkg dpkg-dev fakeroot g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv libacl1 libapt-pkg6.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libfakeroot libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgprofng0 libitm1 liblsan0 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libzstd1 linux-libc-dev lsb-base ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata xz-utils zlib1g 87 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 95.7 MB of archives. After this operation, 4803 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu lunar/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main amd64 diffutils amd64 1:3.8-3 [176 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main amd64 liblzma5 amd64 5.4.1-0.0 [125 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 libcc1-0 amd64 12.2.0-14ubuntu1 [46.5 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main amd64 libgprofng0 amd64 2.40-2ubuntu1 [897 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main amd64 libctf0 amd64 2.40-2ubuntu1 [97.4 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main amd64 libctf-nobfd0 amd64 2.40-2ubuntu1 [100 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2ubuntu1 [2484 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main amd64 libbinutils amd64 2.40-2ubuntu1 [633 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils-common amd64 2.40-2ubuntu1 [236 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 binutils amd64 2.40-2ubuntu1 [3196 B] Get:13 http://ftpmaster.internal/ubuntu lunar/main amd64 gcc-12-base amd64 12.2.0-14ubuntu1 [19.2 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcc-s1 amd64 12.2.0-14ubuntu1 [53.9 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main amd64 libgomp1 amd64 12.2.0-14ubuntu1 [125 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 libitm1 amd64 12.2.0-14ubuntu1 [29.5 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main amd64 libatomic1 amd64 12.2.0-14ubuntu1 [10.4 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 libasan8 amd64 12.2.0-14ubuntu1 [2429 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main amd64 liblsan0 amd64 12.2.0-14ubuntu1 [1061 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main amd64 libtsan2 amd64 12.2.0-14ubuntu1 [2456 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main amd64 libubsan1 amd64 12.2.0-14ubuntu1 [969 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main amd64 libquadmath0 amd64 12.2.0-14ubuntu1 [152 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main amd64 g++-12 amd64 12.2.0-14ubuntu1 [12.0 MB] Get:24 http://ftpmaster.internal/ubuntu lunar/main amd64 libstdc++-12-dev amd64 12.2.0-14ubuntu1 [2157 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 libgcc-12-dev amd64 12.2.0-14ubuntu1 [2577 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main amd64 gcc-12 amd64 12.2.0-14ubuntu1 [21.4 MB] Get:27 http://ftpmaster.internal/ubuntu lunar/main amd64 cpp-12 amd64 12.2.0-14ubuntu1 [10.6 MB] Get:28 http://ftpmaster.internal/ubuntu lunar/main amd64 libstdc++6 amd64 12.2.0-14ubuntu1 [678 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main amd64 libzstd1 amd64 1.5.2+dfsg2-3 [282 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgcrypt20 amd64 1.10.1-3ubuntu1 [529 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit-common all 1:3.0.7-1.1 [5108 B] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit1 amd64 1:3.0.7-1.1 [45.3 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcap2 amd64 1:2.66-3ubuntu1 [28.0 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main amd64 libcrypt-dev amd64 1:4.4.33-2 [113 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main amd64 libcrypt1 amd64 1:4.4.33-2 [80.7 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main amd64 libpcre2-8-0 amd64 10.42-1 [228 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main amd64 libselinux1 amd64 3.4-1build2 [78.0 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main amd64 libperl5.36 amd64 5.36.0-7 [4834 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main amd64 perl amd64 5.36.0-7 [235 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main amd64 perl-base amd64 5.36.0-7 [1779 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main amd64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main amd64 debconf all 1.5.82 [125 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main amd64 libssl3 amd64 3.0.7-1ubuntu1 [1896 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 systemd-sysv amd64 252.4-1ubuntu1 [11.4 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 systemd amd64 252.4-1ubuntu1 [3001 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsystemd-shared amd64 252.4-1ubuntu1 [1771 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsystemd0 amd64 252.4-1ubuntu1 [328 kB] Get:53 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libudev1 amd64 252.4-1ubuntu1 [89.6 kB] Get:54 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libapt-pkg6.0 amd64 2.5.5 [903 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 dpkg amd64 1.21.18ubuntu3 [1332 kB] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 ncurses-bin amd64 6.4-2 [185 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main amd64 sed amd64 4.9-1 [193 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 ncurses-base all 6.4-2 [21.3 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main amd64 sysvinit-utils amd64 3.05-7ubuntu2 [27.4 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main amd64 lsb-base all 11.5 [4296 B] Get:61 http://ftpmaster.internal/ubuntu lunar/main amd64 adduser all 3.129ubuntu1 [59.0 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main amd64 gpgv amd64 2.2.40-1ubuntu2 [137 kB] Get:63 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgnutls30 amd64 3.7.8-4ubuntu1 [986 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 apt amd64 2.5.5 [1378 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main amd64 libsemanage-common all 3.4-1build2 [9774 B] Get:67 http://ftpmaster.internal/ubuntu lunar/main amd64 libsemanage2 amd64 3.4-1build2 [93.2 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libncurses6 amd64 6.4-2 [112 kB] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libncursesw6 amd64 6.4-2 [147 kB] Get:70 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libtinfo6 amd64 6.4-2 [101 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main amd64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main amd64 readline-common all 8.2-1.3 [55.7 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main amd64 libreadline8 amd64 8.2-1.3 [151 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main amd64 libsqlite3-0 amd64 3.40.1-1 [654 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main amd64 openssl amd64 3.0.7-1ubuntu1 [1179 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main amd64 tzdata all 2022g-2ubuntu1 [397 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main amd64 xz-utils amd64 5.4.1-0.0 [240 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main amd64 advancecomp amd64 2.5-1 [180 kB] Get:79 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 dpkg-dev all 1.21.18ubuntu3 [1067 kB] Get:80 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libdpkg-perl all 1.21.18ubuntu3 [247 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main amd64 libfakeroot amd64 1.30.1-1.1ubuntu1 [30.9 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main amd64 fakeroot amd64 1.30.1-1.1ubuntu1 [60.2 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main amd64 gpg amd64 2.2.40-1ubuntu2 [523 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main amd64 gpgconf amd64 2.2.40-1ubuntu2 [93.7 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main amd64 gpg-agent amd64 2.2.40-1ubuntu2 [217 kB] Get:86 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 linux-libc-dev amd64 5.19.0-23.24 [1345 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main amd64 pkgbinarymangler all 151 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 95.7 MB in 1s (63.9 MB/s) (Reading database ... 13093 files and directories currently installed.) 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Setting up libstdc++-12-dev:amd64 (12.2.0-14ubuntu1) ... Setting up binutils (2.40-2ubuntu1) ... Setting up dpkg-dev (1.21.18ubuntu3) ... Setting up gcc-12 (12.2.0-14ubuntu1) ... Setting up g++-12 (12.2.0-14ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-25524220 amd64 lunar-proposed -c chroot:build-PACKAGEBUILD-25524220 --arch=amd64 --dist=lunar-proposed --nolog -A nanopolish_0.14.0-1ubuntu1.dsc Initiating build PACKAGEBUILD-25524220 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-029.buildd +==============================================================================+ | nanopolish 0.14.0-1ubuntu1 (amd64) Thu, 26 Jan 2023 17:32:02 +0000 | +==============================================================================+ Package: nanopolish Version: 0.14.0-1ubuntu1 Source Version: 0.14.0-1ubuntu1 Distribution: lunar-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25524220/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/nanopolish-vbZOZE/resolver-rswvUY' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- nanopolish_0.14.0-1ubuntu1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/nanopolish-vbZOZE/nanopolish-0.14.0' with '<>' I: NOTICE: Log filtering will replace 'build/nanopolish-vbZOZE' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [425 B] Get:5 copy:/<>/apt_archive ./ Packages [509 B] Fetched 1891 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libeigen3-dev libelf1 libexpat1 libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3 libhtscodecs2 libicu71 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libldap2 liblzma-dev libmagic-mgc libmagic1 libminimap2-dev libmpdec3 libnghttp2-14 libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libslow5-0 libslow5-dev libssh-4 libssl-dev libstreamvbyte-dev libstreamvbyte0 libsub-override-perl libsz2 libtool libuchardet0 libxml2 m4 man-db media-types pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.11 python3.11-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libeigen3-doc libmpfrc++-dev libhdf5-doc liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libeigen3-dev libelf1 libexpat1 libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3 libhtscodecs2 libicu71 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libldap2 liblzma-dev libmagic-mgc libmagic1 libminimap2-dev libmpdec3 libnghttp2-14 libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libslow5-0 libslow5-dev libssh-4 libssl-dev libstreamvbyte-dev libstreamvbyte0 libsub-override-perl libsz2 libtool libuchardet0 libxml2 m4 man-db media-types pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.11 python3.11-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded. 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(Reading database ... 13155 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.1-2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.1-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.1-2_amd64.deb ... Unpacking python3.11-minimal (3.11.1-2) ... Setting up libpython3.11-minimal:amd64 (3.11.1-2) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 13469 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.1-0ubuntu1_amd64.deb ... Unpacking python3-minimal (3.11.1-0ubuntu1) ... Selecting previously unselected package media-types. 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Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu10) ... Setting up libhts-dev:amd64 (1.16+ds-3) ... Setting up python3 (3.11.1-0ubuntu1) ... Setting up man-db (2.11.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up python3-lib2to3 (3.10.8-1) ... Setting up libhdf5-hl-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up python3-distutils (3.10.8-1) ... Setting up dh-python (5.20230109) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-fortran-102:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-dev (1.10.8+repack1-1ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libfast5-dev (0.6.5-7build1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (252.4-1ubuntu1) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 arm64 armhf ppc64el riscv64) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:22 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.40-2ubuntu1 dpkg-dev_1.21.18ubuntu3 g++-12_12.2.0-14ubuntu1 gcc-12_12.2.0-14ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-12-dev_12.2.0-14ubuntu1 libstdc++6_12.2.0-14ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.5.5 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu1 binutils-common_2.40-2ubuntu1 binutils-x86-64-linux-gnu_2.40-2ubuntu1 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-14ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_5.20230109 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-3 dpkg_1.21.18ubuntu3 dpkg-dev_1.21.18ubuntu3 dwz_0.15-1 e2fsprogs_1.46.6~rc1-1ubuntu1 fakeroot_1.30.1-1.1ubuntu1 file_1:5.44-2 findutils_4.9.0-3ubuntu1 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-14ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-14ubuntu1 gcc-12-base_12.2.0-14ubuntu1 gettext_0.21-10 gettext-base_0.21-10 gpg_2.2.40-1ubuntu2 gpg-agent_2.2.40-1ubuntu2 gpgconf_2.2.40-1ubuntu2 gpgv_2.2.40-1ubuntu2 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 hdf5-helpers_1.10.8+repack1-1ubuntu1 hostname_3.23ubuntu2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapparmor1_3.0.8-1ubuntu1 libapt-pkg6.0_2.5.5 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-14ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-14ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.40-2ubuntu1 libblkid1_2.38.1-4ubuntu1 libbrotli1_1.0.9-2build7 libbz2-1.0_1.0.8-5build1 libc-bin_2.36-0ubuntu4 libc-dev-bin_2.36-0ubuntu4 libc6_2.36-0ubuntu4 libc6-dev_2.36-0ubuntu4 libcap-ng0_0.8.3-1build1 libcap2_1:2.66-3ubuntu1 libcc1-0_12.2.0-14ubuntu1 libcom-err2_1.46.6~rc1-1ubuntu1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.5.0-6ubuntu3 libctf-nobfd0_2.40-2ubuntu1 libctf0_2.40-2ubuntu1 libcurl3-gnutls_7.87.0-1ubuntu1 libcurl4_7.87.0-1ubuntu1 libcurl4-gnutls-dev_7.87.0-1ubuntu1 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.18ubuntu3 libdw1_0.188-2.1 libeigen3-dev_3.4.0-2ubuntu2 libelf1_0.188-2.1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1ubuntu1 libfakeroot_1.30.1-1.1ubuntu1 libfast5-dev_0.6.5-7build1 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.2.0-14ubuntu1 libgcc-s1_12.2.0-14ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-14ubuntu1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.8-4ubuntu1 libgomp1_12.2.0-14ubuntu1 libgpg-error0_1.46-1 libgprofng0_2.40-2ubuntu1 libgssapi-krb5-2_1.20.1-1build1 libhdf5-103-1_1.10.8+repack1-1ubuntu1 libhdf5-cpp-103-1_1.10.8+repack1-1ubuntu1 libhdf5-dev_1.10.8+repack1-1ubuntu1 libhdf5-fortran-102_1.10.8+repack1-1ubuntu1 libhdf5-hl-100_1.10.8+repack1-1ubuntu1 libhdf5-hl-cpp-100_1.10.8+repack1-1ubuntu1 libhdf5-hl-fortran-100_1.10.8+repack1-1ubuntu1 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-3 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libicu71_71.1-3ubuntu1 libidn2-0_2.3.3-1build1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libitm1_12.2.0-14ubuntu1 libjansson4_2.14-2 libjpeg-dev_8c-2ubuntu10 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg-turbo8-dev_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu10 libjpeg8-dev_8c-2ubuntu10 libjson-c5_0.16-2 libk5crypto3_1.20.1-1build1 libkeyutils1_1.6.3-2 libkmod2_30+20220905-1ubuntu1 libkrb5-3_1.20.1-1build1 libkrb5support0_1.20.1-1build1 libldap2_2.6.3+dfsg-1~exp1ubuntu1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_12.2.0-14ubuntu1 liblz4-1_1.9.4-1 liblzma-dev_5.4.1-0.0 liblzma5_5.4.1-0.0 libmagic-mgc_1:5.44-2 libmagic1_1:5.44-2 libmd0_1.0.4-2 libminimap2-dev_2.24+dfsg-3 libmount1_2.38.1-4ubuntu1 libmpc3_1.3.1-1 libmpdec3_2.5.1-2build2 libmpfr6_4.2.0-1 libncurses6_6.4-2 libncursesw6_6.4-2 libnettle8_3.8.1-2 libnghttp2-14_1.51.0-1 libnpth0_1.6-3build2 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pinentry-curses_1.2.1-1ubuntu1 pkg-config_1.8.1-1ubuntu2 pkgbinarymangler_151 pkgconf_1.8.1-1ubuntu2 pkgconf-bin_1.8.1-1ubuntu2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-7ubuntu1 python3_3.11.1-0ubuntu1 python3-distutils_3.10.8-1 python3-lib2to3_3.10.8-1 python3-minimal_3.11.1-0ubuntu1 python3.11_3.11.1-2 python3.11-minimal_3.11.1-2 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 systemd_252.4-1ubuntu1 systemd-sysv_252.4-1ubuntu1 sysvinit-utils_3.05-7ubuntu2 tar_1.34+dfsg-1.1 tzdata_2022g-2ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 xz-utils_5.4.1-0.0 zlib1g_1:1.2.13.dfsg-1ubuntu4 zlib1g-dev_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: nanopolish Binary: nanopolish Architecture: amd64 arm64 armhf ppc64el riscv64 Version: 0.14.0-1ubuntu1 Maintainer: Ubuntu Developers Uploaders: Andreas Tille Homepage: https://github.com/jts/nanopolish Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/nanopolish Vcs-Git: https://salsa.debian.org/med-team/nanopolish.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev Package-List: nanopolish deb science optional arch=amd64,arm64,armhf,ppc64el,riscv64 Checksums-Sha1: a26c2a1a0f41a0e3fef52dee3d6ef1aea11e0266 4073583 nanopolish_0.14.0.orig.tar.gz 5af42c6351fa76123907c6cc6635ff6c6c2a478e 9120 nanopolish_0.14.0-1ubuntu1.debian.tar.xz Checksums-Sha256: bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78 4073583 nanopolish_0.14.0.orig.tar.gz 748a9f4f488efcaed612ea2844d35d7cd11282e8cb0a1bce47ad841e7ca51866 9120 nanopolish_0.14.0-1ubuntu1.debian.tar.xz Files: 90b445d40348427fd009bea3e04f0249 4073583 nanopolish_0.14.0.orig.tar.gz 61105d478de743f68337caadacb032ad 9120 nanopolish_0.14.0-1ubuntu1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfm2fYq1zA4h6PB3QSRbXqx16OAQFAmPRmsQACgkQSRbXqx16 OAR+Xg//etrjSt21luN11zyelJc135Olt/FtJtq884P3zdSaz/hY8+paeShItrDa EVwFexRRXjXDC3q3NxzVaqTJxhkjJacQ0qq6jPFs+gUH/ttaa/N5HZIP2OdYcnRS 5LfPzDfgBOSg2QX3WuJizRwryEZGuSGZEmmatFZTKweKpAFfrkSwYjxbOGhK1wmU X8StEBl4rODXHwKhsMOQ/uC0tM+IaCE/tuaBOpBBuOb4j2OE1LFte62yHPVHe7/m m8LMVaGLaXrQx34sREwA5gaBCXoguFhTe5Gdb7FS9vKO/jkNhLHdTBQHq/0u2Ug3 vaJEzRNUD8ypO8VB38M0HZrYBfWVa6WekhKnek9oy+80MME1MkOdxwI8PB8x4jOa hY2CYdz/ePDV7KWNhQxlOtCBN7SR05B/8X48MOuge5T9DkEdHO0Nz1HKqqKflJFD mXjOK5hB/bcz6yJzpxp3zLK5DoF57gCSmBpPfqEjItQI7lzmwpB+1ScVmObYWiO5 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link_ext_slow5lib.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-25524220 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25524220 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25524220 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package nanopolish dpkg-buildpackage: info: source version 0.14.0-1ubuntu1 dpkg-buildpackage: info: source distribution lunar dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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/basemods/nanopolish_basemods.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_detect_polyi.o src/nanopolish_fast5_check.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 dh binary --with python3 dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>' rm -f ./.depend g++ -o src/main/nanopolish.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/main/nanopolish.cpp g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/alignment/nanopolish_alignment_db.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/basemods/nanopolish_basemods.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_detect_polyi.cpp src/nanopolish_fast5_check.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_anchor.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/alignment/nanopolish_anchor.cpp g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/alignment/nanopolish_eventalign.cpp g++ -o src/basemods/nanopolish_basemods.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/basemods/nanopolish_basemods.cpp g++ -o src/common/fs_support.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/fs_support.cpp g++ -o src/common/logsum.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/logsum.cpp g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/nanopolish_alphabet.cpp g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/nanopolish_bam_processor.cpp g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/nanopolish_bam_utils.cpp g++ -o src/common/nanopolish_common.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/nanopolish_common.cpp g++ -o src/common/nanopolish_iupac.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/nanopolish_iupac.cpp g++ -o src/common/nanopolish_klcs.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/nanopolish_klcs.cpp g++ -o src/common/nanopolish_variant.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/common/nanopolish_variant.cpp g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/hmm/nanopolish_duration_model.cpp g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/hmm/nanopolish_profile_hmm.cpp g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/hmm/nanopolish_transition_parameters.cpp g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/io/nanopolish_fast5_io.cpp g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/io/nanopolish_fast5_loader.cpp g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/io/nanopolish_fast5_processor.cpp g++ -o src/nanopolish_call_methylation.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_call_methylation.cpp g++ -o src/nanopolish_call_variants.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_call_variants.cpp g++ -o src/nanopolish_detect_polyi.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_detect_polyi.cpp src/nanopolish_detect_polyi.cpp: In function ‘void dpi_estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)’: src/nanopolish_detect_polyi.cpp:1040:39: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 1040 | fprintf(out_fp, "%s\t%s\t%d\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n", | ~^ | | | int | %ld 1041 | read_name.c_str(), ref_name.c_str(), record->core.pos); | ~~~~~~~~~~~~~~~~ | | | long int src/nanopolish_detect_polyi.cpp:1105:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 1105 | fprintf(out_fp, "%s\t%s\t%d\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\t%s\n", | ~^ | | | int | %ld 1106 | read_name.c_str(), ref_name.c_str(), record->core.pos, | ~~~~~~~~~~~~~~~~ | | | long int g++ -o src/nanopolish_fast5_check.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_fast5_check.cpp g++ -o src/nanopolish_haplotype.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_haplotype.cpp g++ -o src/nanopolish_index.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_index.cpp g++ -o src/nanopolish_methyltrain.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_methyltrain.cpp g++ -o src/nanopolish_phase_reads.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_phase_reads.cpp g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_polya_estimator.cpp g++ -o src/nanopolish_raw_loader.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_raw_loader.cpp 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:765:39: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 765 | fprintf(out_fp, "%s\t%s\t%d\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n", | ~^ | | | int | %ld 766 | read_name.c_str(), ref_name.c_str(), record->core.pos); | ~~~~~~~~~~~~~~~~ | | | long int src/nanopolish_polya_estimator.cpp:823:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 823 | fprintf(out_fp, "%s\t%s\t%d\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\n", | ~^ | | | int | %ld 824 | read_name.c_str(), ref_name.c_str(), record->core.pos, | ~~~~~~~~~~~~~~~~ | | | long int g++ -o src/nanopolish_read_db.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_read_db.cpp g++ -o src/nanopolish_scorereads.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_scorereads.cpp g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_squiggle_read.cpp g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp g++ -o src/nanopolish_variant_db.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_variant_db.cpp g++ -o src/nanopolish_vcf2fasta.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/nanopolish_vcf2fasta.cpp g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/pore_model/nanopolish_model_names.cpp g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/pore_model/nanopolish_pore_model_set.cpp g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/pore_model/nanopolish_poremodel.cpp g++ -o src/training_core.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/training_core.cpp cc -o src/thirdparty/fet.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/thirdparty/fet.c cc -o src/thirdparty/scrappie/event_detection.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/thirdparty/scrappie/event_detection.c cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/thirdparty/scrappie/scrappie_common.c cc -o src/thirdparty/stdaln.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/thirdparty/stdaln.c src/thirdparty/stdaln.c: In function ‘aln_local_core’: src/thirdparty/stdaln.c:756:17: warning: ‘free’ called on pointer ‘MEM[(int * *)_694]’ with nonzero offset 4 [-Wfree-nonheap-object] 756 | free(s_array[i]); | ^~~~~~~~~~~~~~~~ g++ -o nanopolish -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.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_detect_polyi.o src/nanopolish_fast5_check.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 -lslow5 -lstreamvbyte -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial make[2]: Leaving directory '/<>' /usr/bin/make nanopolish_test make[2]: Entering directory '/<>' g++ -o src/test/nanopolish_test.o -c -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/test/nanopolish_test.cpp In file included from /usr/include/x86_64-linux-gnu/c++/12/bits/c++allocator.h:33, from /usr/include/c++/12/bits/allocator.h:46, from /usr/include/c++/12/string:41, from src/test/nanopolish_test.cpp:10: In member function ‘std::__new_allocator::deallocate(float*, unsigned long)’, inlined from ‘std::allocator_traits >::deallocate(std::allocator&, float*, unsigned long)’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘std::_Vector_base >::_M_deallocate(float*, unsigned long)’ at /usr/include/c++/12/bits/stl_vector.h:387:19, inlined from ‘std::_Vector_base >::~_Vector_base()’ at /usr/include/c++/12/bits/stl_vector.h:366:15, inlined from ‘std::vector >::~vector()’ at /usr/include/c++/12/bits/stl_vector.h:733:7, inlined from ‘generate_training_data(ParamMixture const&, unsigned long, std::array const&, std::array const&, std::array const&)’ at src/test/nanopolish_test.cpp:534:1: /usr/include/c++/12/bits/new_allocator.h:158:33: warning: ‘operator delete(void*)’ called on pointer ‘_832’ with nonzero offset [4, 658812288346769700] [-Wfree-nonheap-object] 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function ‘std::__new_allocator::allocate(unsigned long, void const*)’, inlined from ‘std::allocator_traits >::allocate(std::allocator&, unsigned long)’ at /usr/include/c++/12/bits/alloc_traits.h:464:28, inlined from ‘std::_Vector_base >::_M_allocate(unsigned long)’ at /usr/include/c++/12/bits/stl_vector.h:378:33, inlined from ‘std::_Vector_base >::_M_create_storage(unsigned long)’ at /usr/include/c++/12/bits/stl_vector.h:395:44, inlined from ‘std::_Vector_base >::_Vector_base(unsigned long, std::allocator const&)’ at /usr/include/c++/12/bits/stl_vector.h:332:26, inlined from ‘std::vector >::vector(unsigned long, float const&, std::allocator const&)’ at /usr/include/c++/12/bits/stl_vector.h:566:47, inlined from ‘generate_training_data(ParamMixture const&, unsigned long, std::array const&, std::array const&, std::array const&)’ at src/test/nanopolish_test.cpp:486:58: /usr/include/c++/12/bits/new_allocator.h:137:55: note: returned from ‘operator new(unsigned long)’ 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ g++ -o nanopolish_test -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu1 -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./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./src/basemods -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.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_detect_polyi.o src/nanopolish_fast5_check.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 -lslow5 -lstreamvbyte -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' echo "Since we need the executable created inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck." Since we need the executable created inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck. make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/nanopolish/ debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install for pl in `find debian -name "*.pl"` ; do \ sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' ${pl} ; \ done for pl in `grep -Rl '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \ sed -i '1s?^#!.*python.*?#!/usr/bin/python3?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian -name *.fast5 -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing dh_dwz -a dh_strip -a debugedit: debian/nanopolish/usr/lib/nanopolish/nanopolish_test: Unknown DWARF DW_FORM_0x1f20 87800d0b48710797ea40efb06223af037afb2621 debugedit: debian/nanopolish/usr/bin/nanopolish: Unknown DWARF DW_FORM_0x1f21 33bd2fc9457aa94a74283bb70c17fde71b615921 dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/nanopolish/usr/lib/nanopolish/nanopolish_test debian/nanopolish/usr/bin/nanopolish were not linked against libstreamvbyte.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 pkgstriptranslations: processing nanopolish (in debian/nanopolish); do_strip: , oemstrip: pkgstriptranslations: processing nanopolish-dbgsym (in debian/.debhelper/nanopolish/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/nanopolish/dbgsym-root/DEBIAN/control, package nanopolish-dbgsym, directory debian/.debhelper/nanopolish/dbgsym-root dpkg-deb: building package 'nanopolish-dbgsym' in 'debian/.debhelper/scratch-space/build-nanopolish/nanopolish-dbgsym_0.14.0-1ubuntu1_amd64.deb'. pkgstripfiles: processing control file: debian/nanopolish/DEBIAN/control, package nanopolish, directory debian/nanopolish pkgstripfiles: Truncating usr/share/doc/nanopolish/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package nanopolish ... pkgstripfiles: No PNG files. dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-1ubuntu1_amd64.deb'. Renaming nanopolish-dbgsym_0.14.0-1ubuntu1_amd64.deb to nanopolish-dbgsym_0.14.0-1ubuntu1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../nanopolish_0.14.0-1ubuntu1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../nanopolish_0.14.0-1ubuntu1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-01-26T17:33:24Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ nanopolish_0.14.0-1ubuntu1_amd64.changes: ----------------------------------------- Format: 1.8 Date: Wed, 25 Jan 2023 11:31:01 -0500 Source: nanopolish Binary: nanopolish Built-For-Profiles: noudeb Architecture: amd64 Version: 0.14.0-1ubuntu1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: William 'jawn-smith' Wilson Description: nanopolish - consensus caller for nanopore sequencing data Changes: nanopolish (0.14.0-1ubuntu1) lunar; urgency=medium . * Disable building on s390x to resolve missing dependencies Checksums-Sha1: 7d2fefb09ac897cf076c12dc43bb6be6197cd502 8310574 nanopolish-dbgsym_0.14.0-1ubuntu1_amd64.ddeb 0ac9e7c729d482c01fbb9e7856b517ccf4b72f42 8062 nanopolish_0.14.0-1ubuntu1_amd64.buildinfo f532b00794ab01cd78a912628ec25d018a955a49 2373564 nanopolish_0.14.0-1ubuntu1_amd64.deb Checksums-Sha256: 6815f801ca3235b4650183522595541dfee53e11fc34abaff1685ccef7b25a43 8310574 nanopolish-dbgsym_0.14.0-1ubuntu1_amd64.ddeb e7573f5e0b40fbb636075b1de92acf731bc9a203bf46a9404ddc9f38d891df42 8062 nanopolish_0.14.0-1ubuntu1_amd64.buildinfo bdfc110a0f1fd7d208f89a6a26b7a214e3ad6862d3980fb7361243efa61383f5 2373564 nanopolish_0.14.0-1ubuntu1_amd64.deb Files: 0021cd0e22461a6a02eb58fd1689cc4f 8310574 debug optional nanopolish-dbgsym_0.14.0-1ubuntu1_amd64.ddeb 090094caec3c8a1a825aa742ec0dfd33 8062 science optional nanopolish_0.14.0-1ubuntu1_amd64.buildinfo 1c209478301a7d1916d09f5e7cb9c3c8 2373564 science optional nanopolish_0.14.0-1ubuntu1_amd64.deb Original-Maintainer: Debian Med Packaging Team /<>/nanopolish_0.14.0-1ubuntu1_amd64.changes.new could not be renamed to /<>/nanopolish_0.14.0-1ubuntu1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: nanopolish Binary: nanopolish nanopolish-dbgsym Architecture: amd64 Version: 0.14.0-1ubuntu1 Checksums-Md5: 0021cd0e22461a6a02eb58fd1689cc4f 8310574 nanopolish-dbgsym_0.14.0-1ubuntu1_amd64.ddeb 1c209478301a7d1916d09f5e7cb9c3c8 2373564 nanopolish_0.14.0-1ubuntu1_amd64.deb Checksums-Sha1: 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3.11.1-2), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sysvinit-utils (= 3.05-7ubuntu2), tar (= 1.34+dfsg-1.1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), xz-utils (= 5.4.1-0.0), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1674664261" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ nanopolish_0.14.0-1ubuntu1_amd64.deb ------------------------------------ new Debian package, version 2.0. size 2373564 bytes: control archive=2085 bytes. 1034 bytes, 19 lines control 2320 bytes, 30 lines md5sums 305 bytes, 12 lines * postinst #!/bin/sh 380 bytes, 12 lines * prerm #!/bin/sh Package: nanopolish Version: 0.14.0-1ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 9386 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libgomp1 (>= 6), libhdf5-103-1, libhts3 (>= 1.10), libslow5-0 (>= 0.5.1), libstdc++6 (>= 11), libstreamvbyte0 (>= 0.4.1), zlib1g (>= 1:1.1.4), python3:any, perl:any Recommends: python3-biopython, python3-pysam Suggests: perl, make Section: science Priority: optional Homepage: https://github.com/jts/nanopolish Description: consensus caller for nanopore sequencing data Nanopolish uses a signal-level hidden Markov model for consensus calling of nanopore genome sequencing data. It can perform signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2023-01-25 16:31 ./ drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/ drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/bin/ -rwxr-xr-x root/root 3894504 2023-01-25 16:31 ./usr/bin/nanopolish -rwxr-xr-x root/root 75 2022-07-02 09:08 ./usr/bin/nanopolish_makerange drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/lib/ drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/lib/nanopolish/ -rwxr-xr-x root/root 2913 2023-01-25 16:31 ./usr/lib/nanopolish/calculate_methylation_frequency.py -rwxr-xr-x root/root 599 2023-01-25 16:31 ./usr/lib/nanopolish/consensus-preprocess.pl -rwxr-xr-x root/root 1044 2023-01-25 16:31 ./usr/lib/nanopolish/consensus.make -rw-r--r-- root/root 923 2023-01-25 16:31 ./usr/lib/nanopolish/convert_all_models.py -rw-r--r-- root/root 2738 2023-01-25 16:31 ./usr/lib/nanopolish/convert_model_to_header.py -rw-r--r-- root/root 2090 2023-01-25 16:31 ./usr/lib/nanopolish/dropmodel.py -rwxr-xr-x root/root 13202 2023-01-25 16:31 ./usr/lib/nanopolish/extract_reads_aligned_to_region.py -rw-r--r-- root/root 2592 2023-01-25 16:31 ./usr/lib/nanopolish/import_ont_model.py -rwxr-xr-x root/root 286 2023-01-25 16:31 ./usr/lib/nanopolish/import_ont_models_from_dir.sh -rwxr-xr-x root/root 1188 2023-01-25 16:31 ./usr/lib/nanopolish/nanopolish_makerange.py -rw-r--r-- root/root 3136 2023-01-25 16:31 ./usr/lib/nanopolish/nanopolish_merge.py -rwxr-xr-x root/root 3755176 2023-01-25 16:31 ./usr/lib/nanopolish/nanopolish_test drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/lib/nanopolish/polya_training/ -rw-r--r-- root/root 4915 2023-01-25 16:31 ./usr/lib/nanopolish/polya_training/dump_signal.py -rw-r--r-- root/root 2248 2022-04-19 15:17 ./usr/lib/nanopolish/polya_training/environment.yml -rw-r--r-- root/root 4739 2023-01-25 16:31 ./usr/lib/nanopolish/polya_training/hmmplot.py -rw-r--r-- root/root 4071 2023-01-25 16:31 ./usr/lib/nanopolish/polya_training/retrain_emission.py -rw-r--r-- root/root 4029 2023-01-25 16:31 ./usr/lib/nanopolish/polya_training/workflow.md -rw-r--r-- root/root 13736 2023-01-25 16:31 ./usr/lib/nanopolish/reestimate_polya_emissions.py -rw-r--r-- root/root 184 2022-04-19 15:17 ./usr/lib/nanopolish/requirements.txt drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/share/ drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/share/doc/nanopolish/ -rw-r--r-- root/root 190 2022-07-02 09:08 ./usr/share/doc/nanopolish/README.Debian -rw-r--r-- root/root 3296 2022-04-19 15:17 ./usr/share/doc/nanopolish/README.md.gz -rw-r--r-- root/root 278 2022-07-02 09:08 ./usr/share/doc/nanopolish/README.test -rw-r--r-- root/root 1195 2023-01-25 16:31 ./usr/share/doc/nanopolish/changelog.Debian.gz -rw-r--r-- root/root 4071 2022-07-02 09:08 ./usr/share/doc/nanopolish/copyright drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/share/doc/nanopolish/examples/ drwxr-xr-x root/root 0 2022-04-19 15:17 ./usr/share/doc/nanopolish/examples/data/ -rw-r--r-- root/root 1850695 2022-04-19 15:17 ./usr/share/doc/nanopolish/examples/data/LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fast5 -rw-r--r-- root/root 487 2022-07-02 09:08 ./usr/share/doc/nanopolish/run-unit-test drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/share/man/ drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/share/man/man1/ -rw-r--r-- root/root 451 2023-01-25 16:31 ./usr/share/man/man1/nanopolish.1.gz drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/share/python3/ drwxr-xr-x root/root 0 2023-01-25 16:31 ./usr/share/python3/runtime.d/ -rwxr-xr-x root/root 141 2023-01-25 16:31 ./usr/share/python3/runtime.d/nanopolish.rtupdate +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 209676 Build-Time: 72 Distribution: lunar-proposed Host Architecture: amd64 Install-Time: 8 Job: nanopolish_0.14.0-1ubuntu1.dsc Machine Architecture: amd64 Package: nanopolish Package-Time: 82 Source-Version: 0.14.0-1ubuntu1 Space: 209676 Status: successful Version: 0.14.0-1ubuntu1 -------------------------------------------------------------------------------- Finished at 2023-01-26T17:33:24Z Build needed 00:01:22, 209676k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25524220 Scanning for processes to kill in build PACKAGEBUILD-25524220