sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | nanopolish 0.14.0-4 (amd64) Sun, 12 Jul 2026 09:43:03 +0000 | +==============================================================================+ Package: nanopolish Version: 0.14.0-4 Source Version: 0.14.0-4 Distribution: perl-5.44-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Sun, 12 Jul 2026 09:43:04 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup nanopolish_0.14.0-4 perl-5.44-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup nanopolish_0.14.0-4 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 12 Jul 2026 09:43:04 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Get:2 http://deb.debian.org/debian unstable InRelease [193 kB] Get:3 http://deb.debian.org/debian sid InRelease [193 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-07-12-0800.19-F-2026-07-12-0800.19.pdiff [20.9 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-07-12-0800.19-F-2026-07-12-0800.19.pdiff [20.9 kB] Get:7 http://deb.debian.org/debian sid/main Sources T-2026-07-12-0800.19-F-2026-07-12-0800.19.pdiff [9277 B] Get:7 http://deb.debian.org/debian sid/main Sources T-2026-07-12-0800.19-F-2026-07-12-0800.19.pdiff [9277 B] Fetched 543 kB in 6s (84.9 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sun, 12 Jul 2026 09:43:12 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/nanopolish_0.14.0-4.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 12 Jul 2026 09:43:12 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/nanopolish-6AVesk/resolver-0hxndL/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/nanopolish-6AVesk/resolver-0hxndL/apt_archive ./ InRelease Get:2 copy:/build/nanopolish-6AVesk/resolver-0hxndL/apt_archive ./ Release [609 B] Ign:3 copy:/build/nanopolish-6AVesk/resolver-0hxndL/apt_archive ./ Release.gpg Get:4 copy:/build/nanopolish-6AVesk/resolver-0hxndL/apt_archive ./ Sources [734 B] Get:5 copy:/build/nanopolish-6AVesk/resolver-0hxndL/apt_archive ./ Packages [773 B] Fetched 2116 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... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian krb5-multidev libaec-dev libaec0 libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1t64 libevent-2.1-7t64 libexpat1 libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhdf5-310 libhdf5-cpp-310 libhdf5-dev libhdf5-fortran-310 libhdf5-hl-310 libhdf5-hl-cpp-310 libhdf5-hl-fortran-310 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libminimap2-dev libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-crypto-ossl0 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf7 libpsl-dev libpsl5t64 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib librtmp-dev librtmp1 libslow5-0t64 libslow5-dev libssh2-1-dev libssh2-1t64 libssl-dev libstreamvbyte-dev libstreamvbyte3 libsz2 libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev libxml2-16 libzstd-dev m4 man-db media-types netbase nettle-dev pkgconf pkgconf-bin po-debconf python3 python3-minimal python3.14 python3.14-minimal sensible-utils tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc doc-base dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev libeigen3-doc libmpfrc++-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-user libhdf5-doc liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.14-venv python3.14-doc binfmt-support Recommended packages: curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl krb5-locales publicsuffix libtasn1-doc libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian krb5-multidev libaec-dev libaec0 libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1t64 libevent-2.1-7t64 libexpat1 libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgssapi-krb5-2 libgssrpc4t64 libhdf5-310 libhdf5-cpp-310 libhdf5-dev libhdf5-fortran-310 libhdf5-hl-310 libhdf5-hl-cpp-310 libhdf5-hl-fortran-310 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libminimap2-dev libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-crypto-ossl0 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf7 libpsl-dev libpsl5t64 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib librtmp-dev librtmp1 libslow5-0t64 libslow5-dev libssh2-1-dev libssh2-1t64 libssl-dev libstreamvbyte-dev libstreamvbyte3 libsz2 libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev libxml2-16 libzstd-dev m4 man-db media-types netbase nettle-dev pkgconf pkgconf-bin po-debconf python3 python3-minimal python3.14 python3.14-minimal sbuild-build-depends-main-dummy sensible-utils tzdata zlib1g-dev 0 upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 45.0 MB/45.3 MB of archives. After this operation, 187 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 libldap-dev amd64 2.6.13+dfsg-1+b1 [308 kB] Get:2 copy:/build/nanopolish-6AVesk/resolver-0hxndL/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.8.2-1 [121 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.6-1 [896 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.6-1 [2416 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.14.6-1 [25.1 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026b-1 [260 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.6-1 [2278 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.6-1 [846 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.14.6-1 [8108 B] Get:13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.14.6-1 [25.1 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1 [50.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 dh-python all 7.20260623 [114 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.6+repack-2+b1 [20.6 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:49 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-3 [58.3 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-3 [40.3 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-3 [41.3 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-3 [54.1 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-3 [125 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.7-1 [22.3 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.7-1 [18.7 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.7-1 [25.2 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-3 [324 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.21.0-2 [416 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.21.0-2 [17.0 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.25.1-1+b1 [619 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.13-1 [496 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-5 [102 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.4-1 [225 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2+b1 [98.6 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.13-1 [1479 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-3 [14.0 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.69.0-1 [128 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.15.0-1 [94.5 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.22.1-1 [20.9 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.22.1-1 [192 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libunistring-dev amd64 1.4.2-1 [651 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.22.0-1 [29.8 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.6.3-1 [3025 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-4 [393 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-3+b2 [372 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.21.0-2 [546 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.22.1-1 [23.3 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.21.0-2 [422 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.25-1 [56.7 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-5 [1034 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.6+repack-2+b1 [1357 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16.1.0-2 [877 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.6+repack-2+b1 [107 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.6+repack-2+b1 [63.3 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.6+repack-2+b1 [38.1 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.6+repack-2+b1 [130 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.6+repack-2+b1 [18.5 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:3.1.3-4 [213 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:3.1.3-4 [356 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:3.1.3-4 [78.8 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.6+repack-2+b1 [3196 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libfast5-dev all 0.6.5-9 [49.1 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds2-1+b2 [1784 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libminimap2-dev amd64 2.27+dfsg-1+b4 [133 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libslow5-0t64 amd64 1.4.0+dfsg-2 [73.6 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libslow5-dev amd64 1.4.0+dfsg-2 [89.1 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libstreamvbyte3 amd64 3.0.0-1 [11.4 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libstreamvbyte-dev amd64 3.0.0-1 [13.2 kB] Preconfiguring packages ... Fetched 45.0 MB in 0s (143 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 15696 files and directories currently installed.) Preparing to unpack .../libexpat1_2.8.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.8.2-1) ... Selecting previously unselected package libpython3.14-minimal:amd64. Preparing to unpack .../libpython3.14-minimal_3.14.6-1_amd64.deb ... Unpacking libpython3.14-minimal:amd64 (3.14.6-1) ... Selecting previously unselected package python3.14-minimal. Preparing to unpack .../python3.14-minimal_3.14.6-1_amd64.deb ... Unpacking python3.14-minimal (3.14.6-1) ... Setting up libpython3.14-minimal:amd64 (3.14.6-1) ... Setting up libexpat1:amd64 (2.8.2-1) ... Setting up python3.14-minimal (3.14.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 16051 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.14.6-1_amd64.deb ... Unpacking python3-minimal (3.14.6-1) ... 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Current default time zone: 'Etc/UTC' Local time is now: Sun Jul 12 09:43:21 UTC 2026. Universal Time is now: Sun Jul 12 09:43:21 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1+nmu1) ... Setting up libunbound8:amd64 (1.25.1-1+b1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libjpeg62-turbo:amd64 (1:3.1.3-4) ... Setting up libgnutls-dane0t64:amd64 (3.8.13-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:3.1.3-4) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libldap-dev:amd64 (2.6.13+dfsg-1+b1) ... Setting up libstreamvbyte-dev:amd64 (3.0.0-1) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1) ... Setting up libssl-dev:amd64 (3.6.3-1) ... Setting up autopoint (1.0-3) ... Setting up libslow5-0t64:amd64 (1.4.0+dfsg-2) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up libidn2-dev:amd64 (2.3.8-5) ... Setting up libgfortran5:amd64 (16.1.0-2) ... 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Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-3) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libtool (2.5.4-11) ... Setting up libpython3.14-stdlib:amd64 (3.14.6-1) ... Setting up libaec-dev:amd64 (1.1.7-1) ... Setting up libjpeg-dev:amd64 (1:3.1.3-4) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Setting up libslow5-dev:amd64 (1.4.0+dfsg-2) ... Setting up libngtcp2-dev:amd64 (1.22.1-1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up libpsl-dev:amd64 (0.22.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up libminimap2-dev (2.27+dfsg-1+b4) ... Setting up libeigen3-dev (3.4.0-5) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-4) ... Setting up libngtcp2-crypto-ossl0:amd64 (1.22.1-1) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up python3.14 (3.14.6-1) ... Setting up libpython3-stdlib:amd64 (3.14.6-1) ... Setting up libgnutls28-dev:amd64 (3.8.13-1) ... Setting up libcurl4-gnutls:amd64 (8.21.0-2) ... Setting up libnghttp2-dev:amd64 (1.69.0-1) ... Setting up libcurl4t64:amd64 (8.21.0-2) ... Setting up po-debconf (1.0.22) ... Setting up libcurl3t64-gnutls:amd64 (8.21.0-2) ... Setting up python3 (3.14.6-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libgssrpc4t64:amd64 (1.22.1-3) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libhdf5-310:amd64 (1.14.6+repack-2+b1) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Setting up libhdf5-fortran-310:amd64 (1.14.6+repack-2+b1) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-3) ... Setting up libhdf5-cpp-310:amd64 (1.14.6+repack-2+b1) ... Setting up dh-python (7.20260623) ... Setting up libhdf5-hl-310:amd64 (1.14.6+repack-2+b1) ... Setting up libkdb5-10t64:amd64 (1.22.1-3) ... Setting up debhelper (14.3) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-3) ... Setting up krb5-multidev:amd64 (1.22.1-3) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.6+repack-2+b1) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.6+repack-2+b1) ... Setting up libkrb5-dev:amd64 (1.22.1-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.21.0-2) ... Setting up libhdf5-dev (1.14.6+repack-2+b1) ... 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 libhts-dev:amd64 (1.22.1+ds2-1+b2) ... Setting up libfast5-dev (0.6.5-9) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (261.1-2) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 12 Jul 2026 09:43:23 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 12 Jul 2026 09:43:23 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-python_7.20260623 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-7 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gnupg_2.4.9-7 gnupg-l10n_2.4.9-7 gpg_2.4.9-7 gpg-agent_2.4.9-7 gpgconf_2.4.9-7 gpgsm_2.4.9-7 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hdf5-helpers_1.14.6+repack-2+b1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-3 libacl1_2.4.0-1 libaec-dev_1.1.7-1 libaec0_1.1.7-1 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbrotli-dev_1.2.0-3 libbrotli1_1.2.0-3 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcc1-0_16.1.0-2 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl3t64-gnutls_8.21.0-2 libcurl4-gnutls_8.21.0-2 libcurl4-gnutls-dev_8.21.0-2 libcurl4t64_8.21.0-2 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdeflate-dev_1.25-1 libdeflate0_1.25-1 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libeigen3-dev_3.4.0-5 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.13-stable-1 libexpat1_2.8.2-1 libfast5-dev_0.6.5-9 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran5_16.1.0-2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libgssapi-krb5-2_1.22.1-3 libgssrpc4t64_1.22.1-3 libhdf5-310_1.14.6+repack-2+b1 libhdf5-cpp-310_1.14.6+repack-2+b1 libhdf5-dev_1.14.6+repack-2+b1 libhdf5-fortran-310_1.14.6+repack-2+b1 libhdf5-hl-310_1.14.6+repack-2+b1 libhdf5-hl-cpp-310_1.14.6+repack-2+b1 libhdf5-hl-fortran-310_1.14.6+repack-2+b1 libhogweed6t64_3.10.2-1+b1 libhts-dev_1.22.1+ds2-1+b2 libhts3t64_1.22.1+ds2-1+b2 libhtscodecs2_1.6.6-1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libidn2-dev_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libjpeg-dev_1:3.1.3-4 libjpeg62-turbo_1:3.1.3-4 libjpeg62-turbo-dev_1:3.1.3-4 libk5crypto3_1.22.1-3 libkadm5clnt-mit12_1.22.1-3 libkadm5srv-mit12_1.22.1-3 libkdb5-10t64_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5-dev_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.0-3 libldap-dev_2.6.13+dfsg-1+b1 libldap2_2.6.13+dfsg-1+b1 liblsan0_16.1.0-2 liblz4-1_1.10.0-10 liblzma-dev_5.8.3-1 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libminimap2-dev_2.27+dfsg-1+b4 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp2-dev_1.69.0-1 libnghttp3-9_1.15.0-1 libnghttp3-dev_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls-dev_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libngtcp2-crypto-ossl0_1.22.1-1 libngtcp2-dev_1.22.1-1 libnpth0t64_1.8-3+b2 libp11-kit-dev_0.26.4-1 libp11-kit0_0.26.4-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc2-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.22.0-1 libpsl5t64_0.22.0-1 libpython3-stdlib_3.14.6-1 libpython3.14-minimal_3.14.6-1 libpython3.14-stdlib_3.14.6-1 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1 libselinux1_3.11-2 libsframe3_2.46.50.20260617-1 libslow5-0t64_1.4.0+dfsg-2 libslow5-dev_1.4.0+dfsg-2 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssh2-1-dev_1.11.1-4 libssh2-1t64_1.11.1-4 libssl-dev_3.6.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libstreamvbyte-dev_3.0.0-1 libstreamvbyte3_3.0.0-1 libsystemd-shared_261.1-2 libsystemd0_261.1-2 libsz2_1.1.7-1 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libtss2-esys-3.0.2-0t64_4.1.3-6 libtss2-mu-4.0.1-0t64_4.1.3-6 libtss2-rc0t64_4.1.3-6 libtss2-sys1t64_4.1.3-6 libtss2-tcti-cmd0t64_4.1.3-6 libtss2-tcti-device0t64_4.1.3-6 libtss2-tcti-mssim0t64_4.1.3-6 libtss2-tcti-swtpm0t64_4.1.3-6 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunbound8_1.25.1-1+b1 libunistring-dev_1.4.2-1 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libxml2-16_2.15.3+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-3+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 media-types_14.0.0 mount_2.42.2-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 netbase_6.5 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc2-1 perl-base_5.44.0~rc2-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc2-1 pinentry-curses_1.3.3-2 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 python3_3.14.6-1 python3-minimal_3.14.6-1 python3.14_3.14.6-1 python3.14-minimal_3.14.6-1 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 systemd_261.1-2 systemd-tpm_261.1-2 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 tpm-udev_4.1.3-6 tzdata_2026b-1 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sun, 12 Jul 2026 09:43:23 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: nanopolish Binary: nanopolish Architecture: any Version: 0.14.0-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/jts/nanopolish Standards-Version: 4.7.4 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-sequence-python3, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev Package-List: nanopolish deb science optional arch=any Checksums-Sha1: a26c2a1a0f41a0e3fef52dee3d6ef1aea11e0266 4073583 nanopolish_0.14.0.orig.tar.gz 64db61002c480a01258c26c72362ad07a931cb9a 9552 nanopolish_0.14.0-4.debian.tar.xz Checksums-Sha256: bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78 4073583 nanopolish_0.14.0.orig.tar.gz c5613b08807aaea90e84c971cd04d33fd7287cd4101a1b6570047ed2302d21da 9552 nanopolish_0.14.0-4.debian.tar.xz Files: 90b445d40348427fd009bea3e04f0249 4073583 nanopolish_0.14.0.orig.tar.gz 865f2da028b8dea69c692e04957454ad 9552 nanopolish_0.14.0-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmoxD9gRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGXuw/8CqoqAtHTQu5jKaG8FjdQtY6GSL9V1bUr 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/usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting nanopolish in /build/nanopolish-6AVesk/nanopolish-0.14.0 dpkg-source: info: unpacking nanopolish_0.14.0.orig.tar.gz dpkg-source: info: unpacking nanopolish_0.14.0-4.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 dpkg-source: info: applying link_ext_slow5lib.patch dpkg-source: info: applying gcc-15.patch dpkg-source: info: applying libeigen5.0.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sun, 12 Jul 2026 09:43:24 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network nanopolish_0.14.0-4 perl-5.44-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network nanopolish_0.14.0-4 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/nanopolish-6AVesk/nanopolish-0.14.0 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-725f1ad3-a529-461a-9b57-8f2b81f52542 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package nanopolish dpkg-buildpackage: info: source version 0.14.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' sed -i~ 's/^.depend: .*/.depend:/' Makefile touch .depend /usr/bin/make clean make[2]: Entering directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' 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 '/build/nanopolish-6AVesk/nanopolish-0.14.0' rm -f .depend mv Makefile~ Makefile make[1]: Leaving directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building nanopolish using existing ../nanopolish_0.14.0.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building nanopolish in ../nanopolish_0.14.0-4.debian.tar.xz dpkg-source: info: building nanopolish in ../nanopolish_0.14.0-4.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' dh_auto_build make -j2 INSTALL="install --strip-program=true" make[2]: Entering directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' rm -f ./.depend g++ -o src/main/nanopolish.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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++ -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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_alignment_db.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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 g++ -o src/nanopolish_fast5_check.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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 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_haplotype.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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 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_raw_loader.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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 g++ -o src/nanopolish_read_db.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 g++ -o nanopolish -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial make[2]: Leaving directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' /usr/bin/make nanopolish_test make[2]: Entering directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' g++ -o src/test/nanopolish_test.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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 g++ -o nanopolish_test -g -O2 -ffile-prefix-map=/build/nanopolish-6AVesk/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++14 -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,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial lto-wrapper: warning: using serial compilation of 6 LTRANS jobs lto-wrapper: note: see the ‘-flto’ option documentation for more information make[2]: Leaving directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' make[1]: Leaving directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' 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 '/build/nanopolish-6AVesk/nanopolish-0.14.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/nanopolish/ debian/rules override_dh_install make[1]: Entering directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' 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 '/build/nanopolish-6AVesk/nanopolish-0.14.0' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 tools:129: replacing shebang in debian/nanopolish/usr/lib/nanopolish/calculate_methylation_frequency.py I: dh_python3 tools:129: replacing shebang in debian/nanopolish/usr/lib/nanopolish/extract_reads_aligned_to_region.py I: dh_python3 tools:129: replacing shebang in debian/nanopolish/usr/lib/nanopolish/nanopolish_makerange.py dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' dh_fixperms find debian -name *.fast5 -exec chmod -x \{\} \; make[1]: Leaving directory '/build/nanopolish-6AVesk/nanopolish-0.14.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/nanopolish/usr/bin/nanopolish debian/nanopolish/usr/lib/nanopolish/nanopolish_test were not linked against libstreamvbyte.so.3 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-4_amd64.deb'. dpkg-deb: building package 'nanopolish-dbgsym' in '../nanopolish-dbgsym_0.14.0-4_amd64.deb'. dpkg-genbuildinfo -O../nanopolish_0.14.0-4_amd64.buildinfo dpkg-genchanges -O../nanopolish_0.14.0-4_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-07-12T09:45:23Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 12 Jul 2026 09:45:23 +0000 | +------------------------------------------------------------------------------+ nanopolish_0.14.0-4_amd64.changes: ---------------------------------- Format: 1.8 Date: Tue, 16 Jun 2026 10:53:02 +0200 Source: nanopolish Binary: nanopolish nanopolish-dbgsym Architecture: source amd64 Version: 0.14.0-4 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: nanopolish - consensus caller for nanopore sequencing data Changes: nanopolish (0.14.0-4) unstable; urgency=medium . * Rebuild against libstreamvbyte3. Checksums-Sha1: aad1651e5eac9a36bb8fb676d6dfa828829cde68 1216 nanopolish_0.14.0-4.dsc 64db61002c480a01258c26c72362ad07a931cb9a 9552 nanopolish_0.14.0-4.debian.tar.xz 30125a8dd79f08e93b0b8e672a9ea87cba4a324b 7825300 nanopolish-dbgsym_0.14.0-4_amd64.deb ae632161a3730dc7994a681ac8619ddeb6d10ebe 8499 nanopolish_0.14.0-4_amd64.buildinfo 349aa275d329eac19ee6b9ffb15b2f774e2804c3 2205784 nanopolish_0.14.0-4_amd64.deb Checksums-Sha256: 82501a812eeca16462ca0dac035fb19d5bb9189ca3ed0f4461b8602ec33491d9 1216 nanopolish_0.14.0-4.dsc c5613b08807aaea90e84c971cd04d33fd7287cd4101a1b6570047ed2302d21da 9552 nanopolish_0.14.0-4.debian.tar.xz d6b8d9f7cd8fe2e2fa051d7a55aea86a54b095546dc3aae9a958f1f28152a1d4 7825300 nanopolish-dbgsym_0.14.0-4_amd64.deb 1f8d8b81e887e631673fa1f016537a9770163499aae7b8c63172e8ce8f10a505 8499 nanopolish_0.14.0-4_amd64.buildinfo 25cd0badaf175d16fa43a336818d5694b6c55eb9333f27df08505b75c518d59d 2205784 nanopolish_0.14.0-4_amd64.deb Files: 22e7a34541ddbb2425c2303f9a6d2400 1216 science 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1216 nanopolish_0.14.0-4.dsc 30125a8dd79f08e93b0b8e672a9ea87cba4a324b 7825300 nanopolish-dbgsym_0.14.0-4_amd64.deb 349aa275d329eac19ee6b9ffb15b2f774e2804c3 2205784 nanopolish_0.14.0-4_amd64.deb Checksums-Sha256: 82501a812eeca16462ca0dac035fb19d5bb9189ca3ed0f4461b8602ec33491d9 1216 nanopolish_0.14.0-4.dsc d6b8d9f7cd8fe2e2fa051d7a55aea86a54b095546dc3aae9a958f1f28152a1d4 7825300 nanopolish-dbgsym_0.14.0-4_amd64.deb 25cd0badaf175d16fa43a336818d5694b6c55eb9333f27df08505b75c518d59d 2205784 nanopolish_0.14.0-4_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 12 Jul 2026 09:45:23 +0000 Build-Path: /build/nanopolish-6AVesk/nanopolish-0.14.0 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-python (= 7.20260623), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-3), gettext-base (= 1.0-3), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hdf5-helpers (= 1.14.6+repack-2+b1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-3), libacl1 (= 2.4.0-1), libaec-dev (= 1.1.7-1), libaec0 (= 1.1.7-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbrotli-dev (= 1.2.0-3), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcc1-0 (= 16.1.0-2), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl3t64-gnutls (= 8.21.0-2), libcurl4-gnutls (= 8.21.0-2), libcurl4-gnutls-dev (= 8.21.0-2), libcurl4t64 (= 8.21.0-2), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdeflate-dev (= 1.25-1), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.7), libeigen3-dev (= 3.4.0-5), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.13-stable-1), libexpat1 (= 2.8.2-1), libfast5-dev (= 0.6.5-9), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgfortran5 (= 16.1.0-2), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgnutls-dane0t64 (= 3.8.13-1), libgnutls28-dev (= 3.8.13-1), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgssapi-krb5-2 (= 1.22.1-3), libgssrpc4t64 (= 1.22.1-3), libhdf5-310 (= 1.14.6+repack-2+b1), libhdf5-cpp-310 (= 1.14.6+repack-2+b1), libhdf5-dev (= 1.14.6+repack-2+b1), libhdf5-fortran-310 (= 1.14.6+repack-2+b1), libhdf5-hl-310 (= 1.14.6+repack-2+b1), libhdf5-hl-cpp-310 (= 1.14.6+repack-2+b1), libhdf5-hl-fortran-310 (= 1.14.6+repack-2+b1), libhogweed6t64 (= 3.10.2-1+b1), libhts-dev (= 1.22.1+ds2-1+b2), libhts3t64 (= 1.22.1+ds2-1+b2), libhtscodecs2 (= 1.6.6-1), libhwasan0 (= 16.1.0-2), libidn2-0 (= 2.3.8-5), libidn2-dev (= 2.3.8-5), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), libjpeg-dev (= 1:3.1.3-4), libjpeg62-turbo (= 1:3.1.3-4), libjpeg62-turbo-dev (= 1:3.1.3-4), libk5crypto3 (= 1.22.1-3), libkadm5clnt-mit12 (= 1.22.1-3), libkadm5srv-mit12 (= 1.22.1-3), libkdb5-10t64 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5-dev (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap-dev (= 2.6.13+dfsg-1+b1), libldap2 (= 2.6.13+dfsg-1+b1), liblsan0 (= 16.1.0-2), liblzma-dev (= 5.8.3-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libminimap2-dev (= 2.27+dfsg-1+b4), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libncursesw6 (= 6.6+20260608-2), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp2-dev (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libnghttp3-dev (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-gnutls-dev (= 1.22.1-1), libngtcp2-crypto-gnutls8 (= 1.22.1-1), libngtcp2-crypto-ossl0 (= 1.22.1-1), libngtcp2-dev (= 1.22.1-1), libp11-kit-dev (= 0.26.4-1), libp11-kit0 (= 0.26.4-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc2-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.22.0-1), libpsl5t64 (= 0.22.0-1), libpython3-stdlib (= 3.14.6-1), libpython3.14-minimal (= 3.14.6-1), libpython3.14-stdlib (= 3.14.6-1), libquadmath0 (= 16.1.0-2), libreadline8t64 (= 8.3-4), librtmp-dev (= 2.6-1), librtmp1 (= 2.6-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.1-1), libselinux1 (= 3.11-2), libsframe3 (= 2.46.50.20260617-1), libslow5-0t64 (= 1.4.0+dfsg-2), libslow5-dev (= 1.4.0+dfsg-2), libsmartcols1 (= 2.42.2-1), libsqlite3-0 (= 3.53.3-1), libssh2-1-dev (= 1.11.1-4), libssh2-1t64 (= 1.11.1-4), libssl-dev (= 3.6.3-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libstreamvbyte-dev (= 3.0.0-1), libstreamvbyte3 (= 3.0.0-1), libsystemd0 (= 261.1-2), libsz2 (= 1.1.7-1), libtasn1-6 (= 4.21.0-2+b1), libtasn1-6-dev (= 4.21.0-2+b1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunbound8 (= 1.25.1-1+b1), libunistring-dev (= 1.4.2-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libxml2-16 (= 2.15.3+dfsg-1), libzstd-dev (= 1.5.7+dfsg-3+b2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), media-types (= 14.0.0), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), netbase (= 6.5), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc2-1), perl-base (= 5.44.0~rc2-1), perl-modules-5.44 (= 5.44.0~rc2-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), python3 (= 3.14.6-1), python3-minimal (= 3.14.6-1), python3.14 (= 3.14.6-1), python3.14-minimal (= 3.14.6-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), tzdata (= 2026b-1), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1781599982" +------------------------------------------------------------------------------+ | Package contents Sun, 12 Jul 2026 09:45:24 +0000 | +------------------------------------------------------------------------------+ nanopolish-dbgsym_0.14.0-4_amd64.deb ------------------------------------ new Debian package, version 2.0. size 7825300 bytes: control archive=648 bytes. 427 bytes, 12 lines control 299 bytes, 3 lines md5sums Package: nanopolish-dbgsym Source: nanopolish Version: 0.14.0-4 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 14374 Depends: nanopolish (= 0.14.0-4) Section: debug Priority: optional Description: debug symbols for nanopolish Build-Ids: 8b28dd7777afbcfe0c9f5c8feb988d77262d0ca0 b3f82dc34437737d3cfeed29a1d75d65137e795c drwxr-xr-x root/root 0 2026-06-16 08:53 ./ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/debug/.build-id/8b/ -rw-r--r-- root/root 6316888 2026-06-16 08:53 ./usr/lib/debug/.build-id/8b/28dd7777afbcfe0c9f5c8feb988d77262d0ca0.debug drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/debug/.build-id/b3/ -rw-r--r-- root/root 6128592 2026-06-16 08:53 ./usr/lib/debug/.build-id/b3/f82dc34437737d3cfeed29a1d75d65137e795c.debug drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 2258984 2026-06-16 08:53 ./usr/lib/debug/.dwz/x86_64-linux-gnu/nanopolish.debug drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/share/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-06-16 08:53 ./usr/share/doc/nanopolish-dbgsym -> nanopolish nanopolish_0.14.0-4_amd64.deb ----------------------------- new Debian package, version 2.0. size 2205784 bytes: control archive=2148 bytes. 964 bytes, 18 lines control 2320 bytes, 30 lines md5sums 313 bytes, 12 lines * postinst #!/bin/sh 413 bytes, 12 lines * prerm #!/bin/sh Package: nanopolish Version: 0.14.0-4 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 9657 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libgomp1 (>= 6), libhdf5-310 (>= 1.14.3), libhts3t64 (>= 1.17), libslow5-0t64 (>= 0.5.1), libstdc++6 (>= 14), libstreamvbyte3 (>= 3.0.0), 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. drwxr-xr-x root/root 0 2026-06-16 08:53 ./ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/bin/ -rwxr-xr-x root/root 4062368 2026-06-16 08:53 ./usr/bin/nanopolish -rwxr-xr-x root/root 75 2026-06-16 08:53 ./usr/bin/nanopolish_makerange drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/nanopolish/ -rwxr-xr-x root/root 2914 2026-06-16 08:53 ./usr/lib/nanopolish/calculate_methylation_frequency.py -rwxr-xr-x root/root 599 2026-06-16 08:53 ./usr/lib/nanopolish/consensus-preprocess.pl -rwxr-xr-x root/root 1044 2026-06-16 08:53 ./usr/lib/nanopolish/consensus.make -rw-r--r-- root/root 923 2026-06-16 08:53 ./usr/lib/nanopolish/convert_all_models.py -rw-r--r-- root/root 2738 2026-06-16 08:53 ./usr/lib/nanopolish/convert_model_to_header.py -rw-r--r-- root/root 2090 2026-06-16 08:53 ./usr/lib/nanopolish/dropmodel.py -rwxr-xr-x root/root 13203 2026-06-16 08:53 ./usr/lib/nanopolish/extract_reads_aligned_to_region.py -rw-r--r-- root/root 2592 2026-06-16 08:53 ./usr/lib/nanopolish/import_ont_model.py -rwxr-xr-x root/root 286 2026-06-16 08:53 ./usr/lib/nanopolish/import_ont_models_from_dir.sh -rwxr-xr-x root/root 1189 2026-06-16 08:53 ./usr/lib/nanopolish/nanopolish_makerange.py -rw-r--r-- root/root 3136 2026-06-16 08:53 ./usr/lib/nanopolish/nanopolish_merge.py -rwxr-xr-x root/root 3865696 2026-06-16 08:53 ./usr/lib/nanopolish/nanopolish_test drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/lib/nanopolish/polya_training/ -rw-r--r-- root/root 4915 2026-06-16 08:53 ./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 2026-06-16 08:53 ./usr/lib/nanopolish/polya_training/hmmplot.py -rw-r--r-- root/root 4071 2026-06-16 08:53 ./usr/lib/nanopolish/polya_training/retrain_emission.py -rw-r--r-- root/root 4029 2026-06-16 08:53 ./usr/lib/nanopolish/polya_training/workflow.md -rw-r--r-- root/root 13736 2026-06-16 08:53 ./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 2026-06-16 08:53 ./usr/share/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/share/doc/nanopolish/ -rw-r--r-- root/root 190 2026-06-16 08:53 ./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 2026-06-16 08:53 ./usr/share/doc/nanopolish/README.test -rw-r--r-- root/root 660 2026-06-16 08:53 ./usr/share/doc/nanopolish/changelog.Debian.gz -rw-r--r-- root/root 4071 2026-06-16 08:53 ./usr/share/doc/nanopolish/copyright drwxr-xr-x root/root 0 2026-06-16 08:53 ./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 2026-06-16 08:53 ./usr/share/doc/nanopolish/run-unit-test drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/share/man/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/share/man/man1/ -rw-r--r-- root/root 451 2026-06-16 08:53 ./usr/share/man/man1/nanopolish.1.gz drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/share/python3/ drwxr-xr-x root/root 0 2026-06-16 08:53 ./usr/share/python3/runtime.d/ -rwxr-xr-x root/root 149 2026-06-16 08:53 ./usr/share/python3/runtime.d/nanopolish.rtupdate +------------------------------------------------------------------------------+ | Post Build Sun, 12 Jul 2026 09:45:25 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 12 Jul 2026 09:45:25 +0000 | +------------------------------------------------------------------------------+ Purging /build/nanopolish-6AVesk Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 12 Jul 2026 09:45:26 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 127220 Build-Time: 119 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 11 Job: /srv/debomatic/incoming/nanopolish_0.14.0-4.dsc Machine Architecture: amd64 Package: nanopolish Package-Time: 140 Source-Version: 0.14.0-4 Space: 127220 Status: successful Version: 0.14.0-4 -------------------------------------------------------------------------------- Finished at 2026-07-12T09:45:23Z Build needed 00:02:20, 127220k disk space