I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 18 02:05:40 -12 2025 I: pbuilder-time-stamp: 1737209140 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [nanopolish_0.14.0-1.dsc] I: copying [./nanopolish_0.14.0.orig.tar.gz] I: copying [./nanopolish_0.14.0-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./nanopolish_0.14.0-1.dsc: unsupported subcommand dpkg-source: info: extracting nanopolish in nanopolish-0.14.0 dpkg-source: info: unpacking nanopolish_0.14.0.orig.tar.gz dpkg-source: info: unpacking nanopolish_0.14.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add-shebang-to-script.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying fix_remaining_python_interpreters.patch dpkg-source: info: applying staticMinimap2Library.patch dpkg-source: info: applying link_ext_slow5lib.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3754063/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='cbbf7d574dd24eda96d263d0a00b44f6' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3754063' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ulJ19JgL/pbuilderrc_H3cd --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ulJ19JgL/b1 --logfile b1/build.log nanopolish_0.14.0-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3754063/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libfast5-dev; however: Package libfast5-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libminimap2-dev; however: Package libminimap2-dev is not installed. pbuilder-satisfydepends-dummy depends on libstreamvbyte-dev; however: Package libstreamvbyte-dev is not installed. pbuilder-satisfydepends-dummy depends on libslow5-dev; however: Package libslow5-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libeigen3-dev{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfast5-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libminimap2-dev{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libslow5-0t64{a} libslow5-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libstreamvbyte-dev{a} libstreamvbyte0{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 142 newly installed, 0 to remove and 0 not upgraded. Need to get 54.2 MB of archives. After unpacking 221 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.1-3 [852 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.1-3 [1990 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-1 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-3 [1912 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-3 [740 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 38 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.23 [919 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.6.0-1 [720 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250108 [113 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 63 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.11.1-1+b1 [331 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.0-2 [3234 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.11.1-1+b1 [461 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-14 [361 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libfast5-dev all 0.6.5-9 [49.1 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libminimap2-dev arm64 2.27+dfsg-1+b3 [114 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libslow5-0t64 arm64 0.7.0+dfsg-3+b2 [54.7 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libslow5-dev arm64 0.7.0+dfsg-3+b2 [79.7 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libstreamvbyte0 arm64 0.4.1-4+b1 [6028 B] Get: 142 http://deb.debian.org/debian unstable/main arm64 libstreamvbyte-dev arm64 0.4.1-4+b1 [6744 B] Fetched 54.2 MB in 1s (107 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (Reading database ... (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 ... 19965 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_arm64.deb ... Unpacking python3.13 (3.13.1-3) ... 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Setting up libgnutls30t64:arm64 (3.8.8-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.8-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up python3.13 (3.13.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.8-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-4) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-4) ... Setting up libgnutls28-dev:arm64 (3.8.8-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... 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Setting up dh-python (6.20250108) ... Setting up libhdf5-hl-cpp-310:arm64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:arm64 (1.14.5+repack-3) ... Setting up libcurl4-gnutls-dev:arm64 (8.11.1-1+b1) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libhts-dev:arm64 (1.20+ds-2) ... Setting up libfast5-dev (0.6.5-9) ... Processing triggers for libc-bin (2.40-5) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/nanopolish-0.14.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../nanopolish_0.14.0-1_source.changes 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 --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' sed -i~ 's/^.depend: .*/.depend:/' Makefile touch .depend /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/nanopolish-0.14.0' rm -f .depend mv Makefile~ Makefile make[1]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' rm -f ./.depend g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/main/nanopolish.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/main/nanopolish.cpp g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_fast5_check.cpp g++ -o src/nanopolish_haplotype.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_polya_estimator.cpp g++ -o src/nanopolish_raw_loader.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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 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_squiggle_read.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/hdf5/serial make[2]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' /usr/bin/make nanopolish_test make[2]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' g++ -o src/test/nanopolish_test.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/aarch64-linux-gnu/hdf5/serial lto-wrapper: warning: using serial compilation of 7 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information make[2]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' make[1]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/nanopolish-0.14.0' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' dh_fixperms find debian -name *.fast5 -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged 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-dbgsym' in '../nanopolish-dbgsym_0.14.0-1_arm64.deb'. dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../nanopolish_0.14.0-1_arm64.buildinfo dpkg-genchanges --build=binary -O../nanopolish_0.14.0-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3754063 and its subdirectories I: Current time: Sat Jan 18 02:08:13 -12 2025 I: pbuilder-time-stamp: 1737209293