sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | nanopolish 0.14.0-1 (amd64) Mon, 18 Aug 2025 14:19:37 +0000 | +==============================================================================+ Package: nanopolish Version: 0.14.0-1 Source Version: 0.14.0-1 Distribution: perl-5.42-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 Mon, 18 Aug 2025 14:19:39 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup nanopolish_0.14.0-1 perl-5.42-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup nanopolish_0.14.0-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 18 Aug 2025 14:19:39 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:2 file:/srv/reprepro perl-5.42/main amd64 Packages [547 kB] Get:3 http://deb.debian.org/debian unstable InRelease [216 kB] Get:4 http://deb.debian.org/debian sid InRelease [216 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-18-0810.54-F-2025-08-16-2015.43.pdiff [176 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-18-0810.54-F-2025-08-16-2015.43.pdiff [176 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-18-0810.54-F-2025-08-16-2015.43.pdiff [126 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-18-0810.54-F-2025-08-16-2015.43.pdiff [126 kB] Fetched 861 kB in 8s (106 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu init-system-helpers libbinutils libctf-nobfd0 libctf0 libgprofng0 libidn2-0 libldap2 libsframe2 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5687 kB/5881 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [194 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.45-4 [810 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.45-4 [89.7 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.45-4 [157 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.45-4 [1042 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.45-4 [266 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.45-4 [539 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.45-4 [2556 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libsframe2 amd64 2.45-4 [79.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-3 [109 kB] Fetched 5687 kB in 0s (61.2 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14971 files and directories currently installed.) Preparing to unpack .../0-libgprofng0_2.45-4_amd64.deb ... Unpacking libgprofng0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../1-libctf0_2.45-4_amd64.deb ... Unpacking libctf0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../2-libctf-nobfd0_2.45-4_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../3-binutils-x86-64-linux-gnu_2.45-4_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.45-4) over (2.45-3) ... Preparing to unpack .../4-binutils_2.45-4_amd64.deb ... Unpacking binutils (2.45-4) over (2.45-3) ... Preparing to unpack .../5-libbinutils_2.45-4_amd64.deb ... Unpacking libbinutils:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../6-binutils-common_2.45-4_amd64.deb ... Unpacking binutils-common:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../7-libsframe2_2.45-4_amd64.deb ... Unpacking libsframe2:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../8-libidn2-0_2.3.8-3_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-3) over (2.3.8-2) ... Preparing to unpack .../9-libldap2_2.6.10+dfsg-1+b1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1+b1) over (2.6.10+dfsg-1) ... Setting up libsframe2:amd64 (2.45-4) ... Setting up binutils-common:amd64 (2.45-4) ... Setting up libctf-nobfd0:amd64 (2.45-4) ... Setting up libidn2-0:amd64 (2.3.8-3) ... Setting up libbinutils:amd64 (2.45-4) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b1) ... Setting up libctf0:amd64 (2.45-4) ... Setting up libgprofng0:amd64 (2.45-4) ... Setting up binutils-x86-64-linux-gnu (2.45-4) ... Setting up binutils (2.45-4) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Fetch source files Mon, 18 Aug 2025 14:19:52 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/nanopolish_0.14.0-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 18 Aug 2025 14:19:53 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/nanopolish-7jbbxo/resolver-nBgxOf/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/nanopolish-7jbbxo/resolver-nBgxOf/apt_archive ./ InRelease Get:2 copy:/build/nanopolish-7jbbxo/resolver-nBgxOf/apt_archive ./ Release [609 B] Ign:3 copy:/build/nanopolish-7jbbxo/resolver-nBgxOf/apt_archive ./ Release.gpg Get:4 copy:/build/nanopolish-7jbbxo/resolver-nBgxOf/apt_archive ./ Sources [724 B] Get:5 copy:/build/nanopolish-7jbbxo/resolver-nBgxOf/apt_archive ./ Packages [763 B] Fetched 2096 B in 0s (138 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: 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-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 libgnutls-openssl27t64 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-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librtmp-dev librtmp1 libslow5-0t64 libslow5-dev libssh2-1-dev libssh2-1t64 libssl-dev libstreamvbyte-dev libstreamvbyte0 libsz2 libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2-16 libzstd-dev m4 man-db media-types netbase nettle-dev pkgconf pkgconf-bin po-debconf python3 python3-minimal python3.13 python3.13-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 gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-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-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 libgnutls-openssl27t64 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-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librtmp-dev librtmp1 libslow5-0t64 libslow5-dev libssh2-1-dev libssh2-1t64 libssl-dev libstreamvbyte-dev libstreamvbyte0 libsz2 libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2-16 libzstd-dev m4 man-db media-types netbase nettle-dev pkgconf pkgconf-bin po-debconf python3 python3-minimal python3.13 python3.13-minimal sbuild-build-depends-main-dummy sensible-utils tzdata zlib1g-dev 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 42.4 MB/42.7 MB of archives. After this operation, 165 MB of additional disk space will be used. Get:1 copy:/build/nanopolish-7jbbxo/resolver-nBgxOf/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B] Get:2 file:/srv/reprepro perl-5.42/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b1 [312 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.6-1 [864 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.6-1 [2218 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 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 2025b-5 [260 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.6-1 [1959 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.6-1 [761 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-1 [94.7 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 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 1.4.19-8 [294 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.25 [91.6 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 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 1.14.1-2 [19.7 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:37 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.1 [640 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 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 1.0.21+nmu1 [248 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.25 [937 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:49 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.4-2 [23.8 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.4-2 [8108 B] Get:58 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.4-2 [21.5 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-2 [598 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.10-2 [458 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.10-2 [458 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-3 [103 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.10-2 [1423 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.2-1 [2957 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.15.0-1 [504 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.15.0-1 [392 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-5 [1034 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-1 [862 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-4 [292 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-4 [72.2 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libfast5-dev all 0.6.5-9 [49.1 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds-1 [474 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds-1 [1778 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libminimap2-dev amd64 2.27+dfsg-1+b3 [131 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libslow5-0t64 amd64 0.7.0+dfsg-3+b6 [66.7 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libslow5-dev amd64 0.7.0+dfsg-3+b6 [80.2 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libstreamvbyte0 amd64 0.4.1-4+b1 [5868 B] Get:120 http://deb.debian.org/debian unstable/main amd64 libstreamvbyte-dev amd64 0.4.1-4+b1 [6676 B] Preconfiguring packages ... Fetched 42.4 MB in 1s (67.9 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 14972 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.6-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.6-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.6-1_amd64.deb ... Unpacking python3.13-minimal (3.13.6-1) ... Setting up libpython3.13-minimal:amd64 (3.13.6-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 15306 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... 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Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.19-8) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libaec0:amd64 (1.1.4-2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Aug 18 14:20:07 UTC 2025. Universal Time is now: Mon Aug 18 14:20:07 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.22.0-2) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libgnutls-dane0t64:amd64 (3.8.10-2) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b1) ... Setting up libstreamvbyte-dev:amd64 (0.4.1-4+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Setting up libssl-dev:amd64 (3.5.2-1) ... Setting up autopoint (0.23.1-2) ... Setting up libslow5-0t64:amd64 (0.7.0+dfsg-3+b6) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libidn2-dev:amd64 (2.3.8-3) ... Setting up libgfortran5:amd64 (15.2.0-1) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libpython3.13-stdlib:amd64 (3.13.6-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libsz2:amd64 (1.1.4-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up python3.13 (3.13.6-1) ... Setting up libaec-dev:amd64 (1.1.4-2) ... Setting up libjpeg-dev:amd64 (1:2.1.5-4) ... Setting up python3 (3.13.5-1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up libslow5-dev:amd64 (0.7.0+dfsg-3+b6) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libminimap2-dev (2.27+dfsg-1+b3) ... Setting up libeigen3-dev (3.4.0-5) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up dh-python (6.20250414) ... Setting up libgnutls28-dev:amd64 (3.8.10-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up libcurl4t64:amd64 (8.15.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up libhts3t64:amd64 (1.22.1+ds-1) ... Setting up libhdf5-fortran-310:amd64 (1.14.5+repack-3) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libhdf5-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up debhelper (13.25) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-3) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.15.0-1) ... Setting up libhdf5-dev (1.14.5+repack-3) ... 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+ds-1) ... Setting up libfast5-dev (0.6.5-9) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 18 Aug 2025 14:20:09 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Mon, 18 Aug 2025 14:20:09 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.45-4 dpkg-dev_1.22.21 g++-14_14.3.0-5 gcc-14_14.3.0-5 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 linux-libc-dev_6.12.38-1 Package versions: adduser_3.152 apt_3.1.4 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.2.37-2+b5 binutils_2.45-4 binutils-common_2.45-4 binutils-gold_2.44-2 binutils-gold-x86-64-linux-gnu_2.44-2 binutils-x86-64-linux-gnu_2.45-4 bsdextrautils_2.41.1-1 bsdutils_1:2.41.1-1 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b3 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-14_14.3.0-5 cpp-14-x86-64-linux-gnu_14.3.0-5 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.25 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_20 dh-python_6.20250414 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.8-2 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.3.0-5 g++-14-x86-64-linux-gnu_14.3.0-5 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.3.0-5 gcc-14-base_14.3.0-5 gcc-14-x86-64-linux-gnu_14.3.0-5 gcc-15-base_15.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gnupg_2.4.8-2 gnupg-l10n_2.4.8-2 gpg_2.4.8-2 gpg-agent_2.4.8-2 gpgconf_2.4.8-2 gpgsm_2.4.8-2 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hdf5-helpers_1.14.5+repack-3 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libaec-dev_1.1.4-2 libaec0_1.1.4-2 libapt-pkg7.0_3.1.4 libarchive-zip-perl_1.68-1 libasan8_15.2.0-1 libassuan9_3.0.2-2 libatomic1_15.2.0-1 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.45-4 libblkid1_2.41.1-1 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-1 libcom-err2_1.47.2-3+b3 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-4 libctf0_2.45-4 libcurl3t64-gnutls_8.15.0-1 libcurl4-gnutls-dev_8.15.0-1 libcurl4t64_8.15.0-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.280 libdebhelper-perl_13.25 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libeigen3-dev_3.4.0-5 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.7.1-2 libfast5-dev_0.6.5-9 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.3.0-5 libgcc-s1_15.2.0-1 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_15.2.0-1 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.10-2 libgnutls-openssl27t64_3.8.10-2 libgnutls28-dev_3.8.10-2 libgnutls30t64_3.8.10-2 libgomp1_15.2.0-1 libgpg-error0_1.55-2 libgprofng0_2.45-4 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libhdf5-310_1.14.5+repack-3 libhdf5-cpp-310_1.14.5+repack-3 libhdf5-dev_1.14.5+repack-3 libhdf5-fortran-310_1.14.5+repack-3 libhdf5-hl-310_1.14.5+repack-3 libhdf5-hl-cpp-310_1.14.5+repack-3 libhdf5-hl-fortran-310_1.14.5+repack-3 libhogweed6t64_3.10.1-1 libhts-dev_1.22.1+ds-1 libhts3t64_1.22.1+ds-1 libhtscodecs2_1.6.1-2 libhwasan0_15.2.0-1 libidn2-0_2.3.8-3 libidn2-dev_2.3.8-3 libisl23_0.27-1 libitm1_15.2.0-1 libjansson4_2.14-2+b3 libjpeg-dev_1:2.1.5-4 libjpeg62-turbo_1:2.1.5-4 libjpeg62-turbo-dev_1:2.1.5-4 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.1-1 libldap-dev_2.6.10+dfsg-1+b1 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-1 liblz4-1_1.10.0-4 liblzma-dev_5.8.1-1 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libminimap2-dev_2.27+dfsg-1+b3 libmount1_2.41.1-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1+b1 libnghttp2-dev_1.64.0-1.1+b1 libnghttp3-9_1.8.0-1 libnghttp3-dev_1.8.0-1 libngtcp2-16_1.11.0-1 libngtcp2-crypto-gnutls-dev_1.11.0-1 libngtcp2-crypto-gnutls8_1.11.0-1 libngtcp2-dev_1.11.0-1 libnpth0t64_1.8-3 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 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libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_15.2.0-1 libubsan1_15.2.0-1 libuchardet0_0.0.8-1+b2 libudev1_258~rc2-2 libunbound8_1.22.0-2 libunistring5_1.3-2 libuuid1_2.41.1-1 libxml2-16_2.14.5+dfsg-0.1 libxxhash0_0.8.3-2 libzstd-dev_1.5.7+dfsg-1 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.38-1 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 media-types_13.0.0 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 netbase_6.5 nettle-dev_3.10.1-1 openssl-provider-legacy_3.5.2-1 passwd_1:4.17.4-2 patch_2.8-2 perl_5.42.0-1 perl-base_5.42.0-1 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-1 pinentry-curses_1.3.2-3 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 python3_3.13.5-1 python3-minimal_3.13.5-1 python3.13_3.13.6-1 python3.13-minimal_3.13.6-1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 tzdata_2025b-5 util-linux_2.41.1-1 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 18 Aug 2025 14:20:09 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: nanopolish Binary: nanopolish Architecture: any Version: 0.14.0-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/jts/nanopolish Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/nanopolish Vcs-Git: https://salsa.debian.org/med-team/nanopolish.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev Package-List: nanopolish deb science optional arch=any Checksums-Sha1: a26c2a1a0f41a0e3fef52dee3d6ef1aea11e0266 4073583 nanopolish_0.14.0.orig.tar.gz 70b1db592822052179b1c679ea8999f0af4c5e94 8976 nanopolish_0.14.0-1.debian.tar.xz Checksums-Sha256: bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78 4073583 nanopolish_0.14.0.orig.tar.gz 6c5a39be2682ee430fcc2daf99c7574adf9f0110d4caa13f29af767a995d5bfe 8976 nanopolish_0.14.0-1.debian.tar.xz Files: 90b445d40348427fd009bea3e04f0249 4073583 nanopolish_0.14.0.orig.tar.gz f33e6f1fb88a7cbe9d018781b5d2758c 8976 nanopolish_0.14.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmLJxmwSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxQFgP/09lwg+fdXMZDQIP7yO14o6+RPrMa9xP v4Ujack8J7iodJ3mqRiDEgggiQFyMjJHs2Qu/25pi0QBhXArcf0RD6UwTmjfURIi gecCqIfCtQieRsBa7m2gNdqIQ8a4DDHEmyQzg7xLSPl/clRHyWSK/KTLM2tfly1E hsW6orjxEDjvewy4xfc/LYp5vBDZuBQR+mOii5NDGdAhNxCgbxeP5inlN9cdu4hu 2RGvgdpuF8Z2/dK6iGZJeNIiB6MRNpcPLvVn+tjnxpon+ejhTISWQzNj5/saur3x 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dpkg-source: info: applying staticMinimap2Library.patch dpkg-source: info: applying link_ext_slow5lib.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 18 Aug 2025 14:20:10 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network nanopolish_0.14.0-1 perl-5.42-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network nanopolish_0.14.0-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-7jbbxo/nanopolish-0.14.0 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-9b2e3295-e2a5-45ac-b64e-55e6852e2571 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 0.14.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/nanopolish-7jbbxo/nanopolish-0.14.0' sed -i~ 's/^.depend: .*/.depend:/' Makefile touch .depend /usr/bin/make clean make[2]: Entering directory '/build/nanopolish-7jbbxo/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-7jbbxo/nanopolish-0.14.0' rm -f .depend mv Makefile~ Makefile make[1]: Leaving directory '/build/nanopolish-7jbbxo/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_0.14.0-1.debian.tar.xz dpkg-source: info: building nanopolish in nanopolish_0.14.0-1.dsc debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/nanopolish-7jbbxo/nanopolish-0.14.0' dh_auto_build make -j2 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/nanopolish-7jbbxo/nanopolish-0.14.0' rm -f ./.depend g++ -o src/main/nanopolish.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/main/nanopolish.cpp g++ -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/basemods/nanopolish_basemods.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_detect_polyi.cpp src/nanopolish_fast5_check.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend; g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_alignment_db.cpp g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_anchor.cpp g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_eventalign.cpp g++ -o src/basemods/nanopolish_basemods.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/basemods/nanopolish_basemods.cpp g++ -o src/common/fs_support.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/fs_support.cpp g++ -o src/common/logsum.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/logsum.cpp g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_alphabet.cpp g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_bam_processor.cpp g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_bam_utils.cpp g++ -o src/common/nanopolish_common.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_common.cpp g++ -o src/common/nanopolish_iupac.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_iupac.cpp g++ -o src/common/nanopolish_klcs.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_klcs.cpp g++ -o src/common/nanopolish_variant.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_variant.cpp g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_duration_model.cpp g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm.cpp g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_transition_parameters.cpp g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_io.cpp g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_loader.cpp g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_processor.cpp g++ -o src/nanopolish_call_methylation.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_call_methylation.cpp g++ -o src/nanopolish_call_variants.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_call_variants.cpp g++ -o src/nanopolish_detect_polyi.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_detect_polyi.cpp g++ -o src/nanopolish_fast5_check.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_fast5_check.cpp 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-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_haplotype.cpp g++ -o src/nanopolish_index.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_index.cpp g++ -o src/nanopolish_methyltrain.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_methyltrain.cpp g++ -o src/nanopolish_phase_reads.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_phase_reads.cpp g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_polya_estimator.cpp 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-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_raw_loader.cpp g++ -o src/nanopolish_read_db.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_read_db.cpp g++ -o src/nanopolish_scorereads.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_scorereads.cpp g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_squiggle_read.cpp g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp g++ -o src/nanopolish_variant_db.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_variant_db.cpp g++ -o src/nanopolish_vcf2fasta.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_vcf2fasta.cpp g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_model_names.cpp g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_pore_model_set.cpp g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_poremodel.cpp g++ -o src/training_core.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/training_core.cpp cc -o src/thirdparty/fet.o -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/nanopolish-7jbbxo/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-7jbbxo/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-7jbbxo/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-7jbbxo/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-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_fast5_check.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -lslow5 -lstreamvbyte -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial make[2]: Leaving directory '/build/nanopolish-7jbbxo/nanopolish-0.14.0' /usr/bin/make nanopolish_test make[2]: Entering directory '/build/nanopolish-7jbbxo/nanopolish-0.14.0' g++ -o src/test/nanopolish_test.o -c -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/test/nanopolish_test.cpp g++ -o nanopolish_test -g -O2 -ffile-prefix-map=/build/nanopolish-7jbbxo/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_fast5_check.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -lslow5 -lstreamvbyte -Wl,-z,relro -Wl,-z,now -L/usr/lib/x86_64-linux-gnu/hdf5/serial lto-wrapper: warning: using serial compilation of 8 LTRANS jobs lto-wrapper: note: see the ‘-flto’ option documentation for more information make[2]: Leaving directory '/build/nanopolish-7jbbxo/nanopolish-0.14.0' make[1]: Leaving directory '/build/nanopolish-7jbbxo/nanopolish-0.14.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/nanopolish-7jbbxo/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-7jbbxo/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-7jbbxo/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-7jbbxo/nanopolish-0.14.0' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 I: dh_python3 tools:114: replacing shebang in debian/nanopolish/usr/lib/nanopolish/calculate_methylation_frequency.py I: dh_python3 tools:114: replacing shebang in debian/nanopolish/usr/lib/nanopolish/extract_reads_aligned_to_region.py I: dh_python3 tools:114: 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-7jbbxo/nanopolish-0.14.0' dh_fixperms find debian -name *.fast5 -exec chmod -x \{\} \; make[1]: Leaving directory '/build/nanopolish-7jbbxo/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.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-1_amd64.deb'. dpkg-deb: building package 'nanopolish-dbgsym' in '../nanopolish-dbgsym_0.14.0-1_amd64.deb'. dpkg-genbuildinfo -O../nanopolish_0.14.0-1_amd64.buildinfo dpkg-genchanges -O../nanopolish_0.14.0-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2025-08-18T14:22:16Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 18 Aug 2025 14:22:16 +0000 | +------------------------------------------------------------------------------+ nanopolish_0.14.0-1_amd64.changes: ---------------------------------- Format: 1.8 Date: Sat, 09 Jul 2022 23:37:52 +0530 Source: nanopolish Binary: nanopolish nanopolish-dbgsym Architecture: source amd64 Version: 0.14.0-1 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: nanopolish - consensus caller for nanopore sequencing data Changes: nanopolish (0.14.0-1) unstable; urgency=medium . * Team Upload. . [ Andreas Tille ] * New upstream version * Standards-Version: 4.6.1 (routine-update) . [ Nilesh Patra ] * Add opt to link against external slow5lib * B-D on libslow5lib * d/rules: export SLOW5LIB=external Checksums-Sha1: ae26e8febe6b41fc05557e9de5ce7dd0ef991c4b 1206 nanopolish_0.14.0-1.dsc a26c2a1a0f41a0e3fef52dee3d6ef1aea11e0266 4073583 nanopolish_0.14.0.orig.tar.gz fb31c4f3b060bce9cf2ef698663d811152c4db08 8984 nanopolish_0.14.0-1.debian.tar.xz 951480908af294813d86d111f65dccdfd6c07f82 7858140 nanopolish-dbgsym_0.14.0-1_amd64.deb ed03fca1dc84bb021c69a903b6eeec8777fd1d17 8372 nanopolish_0.14.0-1_amd64.buildinfo 990956a3e78158d0a025f37d70159c0c9bd5575a 2201880 nanopolish_0.14.0-1_amd64.deb Checksums-Sha256: 7f0631d357ffa50d2989036232b04da756cc52bb6ce3142c5c2a3e965a4e7322 1206 nanopolish_0.14.0-1.dsc bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78 4073583 nanopolish_0.14.0.orig.tar.gz ce4f46dfdc431747cd9ef356091226188c0ab13b9b9dbeb401e74f25dfc0eb26 8984 nanopolish_0.14.0-1.debian.tar.xz fe65bdf0f008d390bfc437e7434e5903d8a6f4fb2cdbec211c2c623bd3bfe15e 7858140 nanopolish-dbgsym_0.14.0-1_amd64.deb fbc9822a52db1f562f4a6454d542f9d4af5cc471f412dfeb65a37adf42712bc4 8372 nanopolish_0.14.0-1_amd64.buildinfo 66738e57544a3555292cb4c31263d25d3d66a0c571cb29f169962a4ef58146a5 2201880 nanopolish_0.14.0-1_amd64.deb Files: 16a6c3f61962368f550b15d247edd471 1206 science optional nanopolish_0.14.0-1.dsc 90b445d40348427fd009bea3e04f0249 4073583 science optional nanopolish_0.14.0.orig.tar.gz 562d420d81ebeb012a6c1cd1e7681a72 8984 science optional nanopolish_0.14.0-1.debian.tar.xz 03246af8e49b5cb70109ea709fe0f3b5 7858140 debug optional nanopolish-dbgsym_0.14.0-1_amd64.deb cac2769df14df4ba149140d79b42be7f 8372 science optional nanopolish_0.14.0-1_amd64.buildinfo ee444e0727923325aba25de48e0f8a40 2201880 science optional nanopolish_0.14.0-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 18 Aug 2025 14:22:16 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: nanopolish Binary: nanopolish nanopolish-dbgsym Architecture: amd64 source Version: 0.14.0-1 Checksums-Md5: 16a6c3f61962368f550b15d247edd471 1206 nanopolish_0.14.0-1.dsc 03246af8e49b5cb70109ea709fe0f3b5 7858140 nanopolish-dbgsym_0.14.0-1_amd64.deb ee444e0727923325aba25de48e0f8a40 2201880 nanopolish_0.14.0-1_amd64.deb Checksums-Sha1: ae26e8febe6b41fc05557e9de5ce7dd0ef991c4b 1206 nanopolish_0.14.0-1.dsc 951480908af294813d86d111f65dccdfd6c07f82 7858140 nanopolish-dbgsym_0.14.0-1_amd64.deb 990956a3e78158d0a025f37d70159c0c9bd5575a 2201880 nanopolish_0.14.0-1_amd64.deb Checksums-Sha256: 7f0631d357ffa50d2989036232b04da756cc52bb6ce3142c5c2a3e965a4e7322 1206 nanopolish_0.14.0-1.dsc fe65bdf0f008d390bfc437e7434e5903d8a6f4fb2cdbec211c2c623bd3bfe15e 7858140 nanopolish-dbgsym_0.14.0-1_amd64.deb 66738e57544a3555292cb4c31263d25d3d66a0c571cb29f169962a4ef58146a5 2201880 nanopolish_0.14.0-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 18 Aug 2025 14:22:15 +0000 Build-Path: /build/nanopolish-7jbbxo/nanopolish-0.14.0 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.2.37-2+b5), binutils (= 2.45-4), binutils-common (= 2.45-4), binutils-x86-64-linux-gnu (= 2.45-4), bsdextrautils (= 2.41.1-1), bsdutils (= 1:2.41.1-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), comerr-dev (= 2.1-1.47.2-3+b3), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-14 (= 14.3.0-5), cpp-14-x86-64-linux-gnu (= 14.3.0-5), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.25), debianutils (= 5.23.2), dh-autoreconf (= 20), dh-python (= 6.20250414), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.3.0-5), g++-14-x86-64-linux-gnu (= 14.3.0-5), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.3.0-5), gcc-14-base (= 14.3.0-5), gcc-14-x86-64-linux-gnu (= 14.3.0-5), gcc-15-base (= 15.2.0-1), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hdf5-helpers (= 1.14.5+repack-3), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-5), libacl1 (= 2.3.2-2+b1), libaec-dev (= 1.1.4-2), libaec0 (= 1.1.4-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-1), libatomic1 (= 15.2.0-1), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.45-4), libblkid1 (= 2.41.1-1), libbrotli-dev (= 1.1.0-2+b7), libbrotli1 (= 1.1.0-2+b7), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcc1-0 (= 15.2.0-1), libcom-err2 (= 1.47.2-3+b3), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-4), libctf0 (= 2.45-4), libcurl3t64-gnutls (= 8.15.0-1), libcurl4-gnutls-dev (= 8.15.0-1), libcurl4t64 (= 8.15.0-1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.25), libdeflate-dev (= 1.23-2), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.21), libeigen3-dev (= 3.4.0-5), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libexpat1 (= 2.7.1-2), libfast5-dev (= 0.6.5-9), libffi8 (= 3.4.8-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-14-dev (= 14.3.0-5), libgcc-s1 (= 15.2.0-1), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran5 (= 15.2.0-1), libgmp-dev (= 2:6.3.0+dfsg-3), libgmp10 (= 2:6.3.0+dfsg-3), libgmpxx4ldbl (= 2:6.3.0+dfsg-3), libgnutls-dane0t64 (= 3.8.10-2), libgnutls-openssl27t64 (= 3.8.10-2), libgnutls28-dev (= 3.8.10-2), libgnutls30t64 (= 3.8.10-2), libgomp1 (= 15.2.0-1), libgprofng0 (= 2.45-4), libgssapi-krb5-2 (= 1.21.3-5), libgssrpc4t64 (= 1.21.3-5), libhdf5-310 (= 1.14.5+repack-3), libhdf5-cpp-310 (= 1.14.5+repack-3), libhdf5-dev (= 1.14.5+repack-3), libhdf5-fortran-310 (= 1.14.5+repack-3), libhdf5-hl-310 (= 1.14.5+repack-3), libhdf5-hl-cpp-310 (= 1.14.5+repack-3), libhdf5-hl-fortran-310 (= 1.14.5+repack-3), libhogweed6t64 (= 3.10.1-1), libhts-dev (= 1.22.1+ds-1), libhts3t64 (= 1.22.1+ds-1), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 15.2.0-1), libidn2-0 (= 2.3.8-3), libidn2-dev (= 2.3.8-3), libisl23 (= 0.27-1), libitm1 (= 15.2.0-1), libjansson4 (= 2.14-2+b3), libjpeg-dev (= 1:2.1.5-4), libjpeg62-turbo (= 1:2.1.5-4), libjpeg62-turbo-dev (= 1:2.1.5-4), libk5crypto3 (= 1.21.3-5), libkadm5clnt-mit12 (= 1.21.3-5), libkadm5srv-mit12 (= 1.21.3-5), libkdb5-10t64 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5-dev (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblastlog2-2 (= 2.41.1-1), libldap-dev (= 2.6.10+dfsg-1+b1), libldap2 (= 2.6.10+dfsg-1+b1), liblsan0 (= 15.2.0-1), liblzma-dev (= 5.8.1-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libminimap2-dev (= 2.27+dfsg-1+b3), libmount1 (= 2.41.1-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libncursesw6 (= 6.5+20250216-2), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1.1+b1), libnghttp2-dev (= 1.64.0-1.1+b1), libnghttp3-9 (= 1.8.0-1), libnghttp3-dev (= 1.8.0-1), libngtcp2-16 (= 1.11.0-1), libngtcp2-crypto-gnutls-dev (= 1.11.0-1), libngtcp2-crypto-gnutls8 (= 1.11.0-1), libngtcp2-dev (= 1.11.0-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.42 (= 5.42.0-1), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libpython3-stdlib (= 3.13.5-1), libpython3.13-minimal (= 3.13.6-1), libpython3.13-stdlib (= 3.13.6-1), libquadmath0 (= 15.2.0-1), libreadline8t64 (= 8.2-6), librtmp-dev (= 2.4+20151223.gitfa8646d.1-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-3), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe2 (= 2.45-4), libslow5-0t64 (= 0.7.0+dfsg-3+b6), libslow5-dev (= 0.7.0+dfsg-3+b6), libsmartcols1 (= 2.41.1-1), libsqlite3-0 (= 3.46.1-7), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.5.2-1), libssl3t64 (= 3.5.2-1), libstdc++-14-dev (= 14.3.0-5), libstdc++6 (= 15.2.0-1), libstreamvbyte-dev (= 0.4.1-4+b1), libstreamvbyte0 (= 0.4.1-4+b1), libsystemd0 (= 258~rc2-2), libsz2 (= 1.1.4-2), libtasn1-6 (= 4.20.0-2), libtasn1-6-dev (= 4.20.0-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 15.2.0-1), libubsan1 (= 15.2.0-1), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 258~rc2-2), libunbound8 (= 1.22.0-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41.1-1), libxml2-16 (= 2.14.5+dfsg-0.1), libzstd-dev (= 1.5.7+dfsg-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.38-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), media-types (= 13.0.0), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), netbase (= 6.5), nettle-dev (= 3.10.1-1), openssl-provider-legacy (= 3.5.2-1), patch (= 2.8-2), perl (= 5.42.0-1), perl-base (= 5.42.0-1), perl-modules-5.42 (= 5.42.0-1), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), python3 (= 3.13.5-1), python3-minimal (= 3.13.5-1), python3.13 (= 3.13.6-1), python3.13-minimal (= 3.13.6-1), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), tzdata (= 2025b-5), util-linux (= 2.41.1-1), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1657390072" +------------------------------------------------------------------------------+ | Package contents Mon, 18 Aug 2025 14:22:16 +0000 | +------------------------------------------------------------------------------+ nanopolish-dbgsym_0.14.0-1_amd64.deb ------------------------------------ new Debian package, version 2.0. size 7858140 bytes: control archive=648 bytes. 427 bytes, 12 lines control 299 bytes, 3 lines md5sums Package: nanopolish-dbgsym Source: nanopolish Version: 0.14.0-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 14400 Depends: nanopolish (= 0.14.0-1) Section: debug Priority: optional Description: debug symbols for nanopolish Build-Ids: a08b6cdbb322f3fb79a8f9ee3e28906f4528fade c93a68feb59cb66ad157a4b8fa5d1ebd66d39b2b drwxr-xr-x root/root 0 2022-07-09 18:07 ./ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.build-id/a0/ -rw-r--r-- root/root 6151632 2022-07-09 18:07 ./usr/lib/debug/.build-id/a0/8b6cdbb322f3fb79a8f9ee3e28906f4528fade.debug drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.build-id/c9/ -rw-r--r-- root/root 6307936 2022-07-09 18:07 ./usr/lib/debug/.build-id/c9/3a68feb59cb66ad157a4b8fa5d1ebd66d39b2b.debug drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 2270688 2022-07-09 18:07 ./usr/lib/debug/.dwz/x86_64-linux-gnu/nanopolish.debug drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-07-09 18:07 ./usr/share/doc/nanopolish-dbgsym -> nanopolish nanopolish_0.14.0-1_amd64.deb ----------------------------- new Debian package, version 2.0. size 2201880 bytes: control archive=2128 bytes. 964 bytes, 18 lines control 2320 bytes, 30 lines md5sums 305 bytes, 12 lines * postinst #!/bin/sh 380 bytes, 12 lines * prerm #!/bin/sh Package: nanopolish Version: 0.14.0-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 9642 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), libstreamvbyte0 (>= 0.4.1), zlib1g (>= 1:1.1.4), python3:any, perl:any Recommends: python3-biopython, python3-pysam Suggests: perl, make Section: science Priority: optional Homepage: https://github.com/jts/nanopolish Description: consensus caller for nanopore sequencing data Nanopolish uses a signal-level hidden Markov model for consensus calling of nanopore genome sequencing data. It can perform signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more. drwxr-xr-x root/root 0 2022-07-09 18:07 ./ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/bin/ -rwxr-xr-x root/root 4045984 2022-07-09 18:07 ./usr/bin/nanopolish -rwxr-xr-x root/root 75 2022-07-02 09:08 ./usr/bin/nanopolish_makerange drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/nanopolish/ -rwxr-xr-x root/root 2914 2022-07-09 18:07 ./usr/lib/nanopolish/calculate_methylation_frequency.py -rwxr-xr-x root/root 599 2022-07-09 18:07 ./usr/lib/nanopolish/consensus-preprocess.pl -rwxr-xr-x root/root 1044 2022-07-09 18:07 ./usr/lib/nanopolish/consensus.make -rw-r--r-- root/root 923 2022-07-09 18:07 ./usr/lib/nanopolish/convert_all_models.py -rw-r--r-- root/root 2738 2022-07-09 18:07 ./usr/lib/nanopolish/convert_model_to_header.py -rw-r--r-- root/root 2090 2022-07-09 18:07 ./usr/lib/nanopolish/dropmodel.py -rwxr-xr-x root/root 13203 2022-07-09 18:07 ./usr/lib/nanopolish/extract_reads_aligned_to_region.py -rw-r--r-- root/root 2592 2022-07-09 18:07 ./usr/lib/nanopolish/import_ont_model.py -rwxr-xr-x root/root 286 2022-07-09 18:07 ./usr/lib/nanopolish/import_ont_models_from_dir.sh -rwxr-xr-x root/root 1189 2022-07-09 18:07 ./usr/lib/nanopolish/nanopolish_makerange.py -rw-r--r-- root/root 3136 2022-07-09 18:07 ./usr/lib/nanopolish/nanopolish_merge.py -rwxr-xr-x root/root 3865696 2022-07-09 18:07 ./usr/lib/nanopolish/nanopolish_test drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/nanopolish/polya_training/ -rw-r--r-- root/root 4915 2022-07-09 18:07 ./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 2022-07-09 18:07 ./usr/lib/nanopolish/polya_training/hmmplot.py -rw-r--r-- root/root 4071 2022-07-09 18:07 ./usr/lib/nanopolish/polya_training/retrain_emission.py -rw-r--r-- root/root 4029 2022-07-09 18:07 ./usr/lib/nanopolish/polya_training/workflow.md -rw-r--r-- root/root 13736 2022-07-09 18:07 ./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 2022-07-09 18:07 ./usr/share/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/doc/nanopolish/ -rw-r--r-- root/root 190 2022-07-02 09:08 ./usr/share/doc/nanopolish/README.Debian -rw-r--r-- root/root 3296 2022-04-19 15:17 ./usr/share/doc/nanopolish/README.md.gz -rw-r--r-- root/root 278 2022-07-02 09:08 ./usr/share/doc/nanopolish/README.test -rw-r--r-- root/root 1379 2022-07-09 18:07 ./usr/share/doc/nanopolish/changelog.Debian.gz -rw-r--r-- root/root 4071 2022-07-02 09:08 ./usr/share/doc/nanopolish/copyright drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/doc/nanopolish/examples/ drwxr-xr-x root/root 0 2022-04-19 15:17 ./usr/share/doc/nanopolish/examples/data/ -rw-r--r-- root/root 1850695 2022-04-19 15:17 ./usr/share/doc/nanopolish/examples/data/LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fast5 -rw-r--r-- root/root 487 2022-07-02 09:08 ./usr/share/doc/nanopolish/run-unit-test drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/man/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/man/man1/ -rw-r--r-- root/root 451 2022-07-09 18:07 ./usr/share/man/man1/nanopolish.1.gz drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/python3/ drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/python3/runtime.d/ -rwxr-xr-x root/root 141 2022-07-09 18:07 ./usr/share/python3/runtime.d/nanopolish.rtupdate +------------------------------------------------------------------------------+ | Post Build Mon, 18 Aug 2025 14:22:18 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 18 Aug 2025 14:22:18 +0000 | +------------------------------------------------------------------------------+ Purging /build/nanopolish-7jbbxo Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 18 Aug 2025 14:22:19 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 131112 Build-Time: 126 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 16 Job: /srv/debomatic/incoming/nanopolish_0.14.0-1.dsc Machine Architecture: amd64 Package: nanopolish Package-Time: 159 Source-Version: 0.14.0-1 Space: 131112 Status: successful Version: 0.14.0-1 -------------------------------------------------------------------------------- Finished at 2025-08-18T14:22:16Z Build needed 00:02:39, 131112k disk space