Fri Mar 14 03:06:54 UTC 2025 I: starting to build nanopolish/trixie/amd64 on jenkins on '2025-03-14 03:06' Fri Mar 14 03:06:54 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_7/49924/console.log Fri Mar 14 03:06:54 UTC 2025 I: Downloading source for trixie/nanopolish=0.14.0-1 --2025-03-14 03:06:55-- http://deb.debian.org/debian/pool/main/n/nanopolish/nanopolish_0.14.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2114 (2.1K) [text/prs.lines.tag] Saving to: ‘nanopolish_0.14.0-1.dsc’ 0K .. 100% 301M=0s 2025-03-14 03:06:55 (301 MB/s) - ‘nanopolish_0.14.0-1.dsc’ saved [2114/2114] Fri Mar 14 03:06:55 UTC 2025 I: nanopolish_0.14.0-1.dsc -----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 PO/mHZLJCpfrHY2aXGL+nQr7Em0584uLZFH0YTCHBwlBBxhntgND9bHyhT6BbFdN MVAJTiIdYyH8krbOLSRv/KhDrbqcB03T5kxvUpvtB26GMiTtApoBFhikwLc8E8bd 9VzzRe2g9zaDZpd829n8ebjR0WfJDxpQV0JDe6X9r+KPVzvwCrO3fFc7/k2kcqIm O7xhU+28qbd29TbVWLlusXOczkJYbVKCDOCy860LXp4rrZ5O+5bpvNcTHIJOA3d9 HXIe4NwJRTvf/d52Ax/rG6GRZ8KVpjdRptVuUEudMAbuFkqidFz3cVaEN658xxEN VhXxVMi688dIYZYxcKq+7BNr6X79JXo6uUHzgaxT0+ueYe2oq4my+cxfAxtIo6vq 4aSdl//rZLAg =W3aC -----END PGP SIGNATURE----- Fri Mar 14 03:06:55 UTC 2025 I: Checking whether the package is not for us Fri Mar 14 03:06:55 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Fri Mar 14 03:06:55 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Fri Mar 14 03:17:15 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 13 15:06:58 -12 2025 I: pbuilder-time-stamp: 1741921618 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/2781272/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='29db43c7b463468cad564e3b048f97e6' 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='2781272' 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.o9Yulkhq/pbuilderrc_44aD --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.o9Yulkhq/b1 --logfile b1/build.log nanopolish_0.14.0-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2781272/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: amd64 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 ... 19802 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-minimal{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, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 54.7 MB of archives. After unpacking 208 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 38 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250308 [115 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 52 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-1 [109 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.8-1 [102 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3.1 [292 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3.1 [72.0 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libfast5-dev all 0.6.5-9 [49.1 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libminimap2-dev amd64 2.27+dfsg-1+b3 [131 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libslow5-0t64 amd64 0.7.0+dfsg-3+b6 [66.7 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libslow5-dev amd64 0.7.0+dfsg-3+b6 [80.2 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libstreamvbyte0 amd64 0.4.1-4+b1 [5868 B] Get: 131 http://deb.debian.org/debian trixie/main amd64 libstreamvbyte-dev amd64 0.4.1-4+b1 [6676 B] Fetched 54.7 MB in 2s (33.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (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 ... 19802 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 20136 files and directories currently installed.) 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.2-2_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.2-2) ... Setting up python3-minimal (3.13.2-2) ... Selecting previously unselected package python3. (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 ... 21146 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.2-2_amd64.deb ... Unpacking python3 (3.13.2-2) ... Selecting previously unselected package sensible-utils. 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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 amd64 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 -j20 "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 -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/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 -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++ -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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 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/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 -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/reproducible-path/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 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/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 -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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/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 -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/reproducible-path/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/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: package could avoid a useless dependency if debian/nanopolish/usr/lib/nanopolish/nanopolish_test debian/nanopolish/usr/bin/nanopolish were not linked against libstreamvbyte.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb 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 --build=binary -O../nanopolish_0.14.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../nanopolish_0.14.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/2781272 and its subdirectories I: Current time: Thu Mar 13 15:17:13 -12 2025 I: pbuilder-time-stamp: 1741922233 Fri Mar 14 03:17:15 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Fri Mar 14 03:17:15 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Fri Mar 14 03:20:45 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Fri Mar 14 03:20:46 UTC 2025 I: 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: amd64 Version: 0.14.0-1 Distribution: unstable 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: fec14313888bd4aadd9f9326b4c1c98fc8d6b57a 7848972 nanopolish-dbgsym_0.14.0-1_amd64.deb 3ff94712f07eb5ca86cc743048b00d2135ccf7c4 8148 nanopolish_0.14.0-1_amd64.buildinfo 10c88e19e6f0c4f4b3d706a194ac0e029f55f816 2202184 nanopolish_0.14.0-1_amd64.deb Checksums-Sha256: 7332e090576d14de9a51e118d3c0e2431c58da5b91eb6dc14f133506a3d64ba5 7848972 nanopolish-dbgsym_0.14.0-1_amd64.deb 14d270a8504d071ca7128294e385a35b7a2c3ded1c54aacda9e5d3130bbb2310 8148 nanopolish_0.14.0-1_amd64.buildinfo a4548209dc466f7379ca87e3b6d58ac661281011733b90389a1560970080d2a0 2202184 nanopolish_0.14.0-1_amd64.deb Files: 823b1082f02d8c06998c83453d32a4ee 7848972 debug optional nanopolish-dbgsym_0.14.0-1_amd64.deb b121d426a37ab67dd149831a19422c6c 8148 science optional nanopolish_0.14.0-1_amd64.buildinfo 6352104e5b94131fcd981a96d44a0758 2202184 science optional nanopolish_0.14.0-1_amd64.deb Fri Mar 14 03:20:47 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_7-49924.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.o9Yulkhq/nanopolish_0.14.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.o9Yulkhq/nanopolish_0.14.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.o9Yulkhq/nanopolish_0.14.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.o9Yulkhq/b1/nanopolish_0.14.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.o9Yulkhq/b2/nanopolish_0.14.0-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.004s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 250ms CPU time consumed: 250ms Fri Mar 14 03:20:59 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Fri Mar 14 03:20:59 UTC 2025 I: nanopolish from trixie built successfully and reproducibly on amd64. Fri Mar 14 03:21:00 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Mar 14 03:21:00 UTC 2025 I: Submitting 12K b1/nanopolish_0.14.0-1_amd64.buildinfo.asc Fri Mar 14 03:21:01 UTC 2025 I: Submitting 12K b2/nanopolish_0.14.0-1_amd64.buildinfo.asc Fri Mar 14 03:21:02 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Mar 14 03:21:02 UTC 2025 I: Done submitting .buildinfo files. Fri Mar 14 03:21:02 UTC 2025 I: Removing signed nanopolish_0.14.0-1_amd64.buildinfo.asc files: removed './b1/nanopolish_0.14.0-1_amd64.buildinfo.asc' removed './b2/nanopolish_0.14.0-1_amd64.buildinfo.asc'