I: pbuilder: network access will be disabled during build I: Current time: Fri Jan 10 03:42:16 +14 2025 I: pbuilder-time-stamp: 1736430136 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/30279/tmp/hooks/D01_modify_environment starting debug: Running on virt64b. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 9 13:42 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/30279/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/30279/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=59f5b0339a73474d97fc5e20a1886ee4 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=30279 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.JulM1KKp/pbuilderrc_T3el --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JulM1KKp/b2 --logfile b2/build.log nanopolish_0.14.0-1.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) 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/30279/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: armhf 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 ... 19561 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-2.5-0{a} libldap-dev{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 52.0 MB of archives. After unpacking 181 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libpython3.13-minimal armhf 3.13.1-3 [844 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf python3.13-minimal armhf 3.13.1-3 [1840 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf tzdata all 2024b-5 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libffi8 armhf 3.4.6-1 [20.0 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-6 [146 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libpython3.13-stdlib armhf 3.13.1-3 [1850 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf python3.13 armhf 3.13.1-3 [740 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-4 [196 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-14 [84.4 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-4 [723 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf comerr-dev armhf 2.1-1.47.2-1 [55.1 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.23 [90.6 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libtool all 2.5.4-2 [539 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 38 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-4 [1489 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf debhelper all 13.23 [919 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf python3-autocommand all 2.2.2-3 [13.6 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf python3-typeguard all 4.4.1-1 [37.0 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf python3-inflect all 7.3.1-2 [32.4 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf python3-jaraco.context all 6.0.0-1 [7984 B] Get: 53 http://deb.debian.org/debian unstable/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf python3-pkg-resources all 75.6.0-1 [222 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf python3-zipp all 3.21.0-1 [10.6 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf python3-setuptools all 75.6.0-1 [720 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf dh-python all 6.20250108 [113 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf hdf5-helpers armhf 1.14.5+repack-3 [26.6 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 63 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libgssrpc4t64 armhf 1.21.3-3 [52.5 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libkadm5clnt-mit12 armhf 1.21.3-3 [37.0 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libkdb5-10t64 armhf 1.21.3-3 [37.1 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libkadm5srv-mit12 armhf 1.21.3-3 [46.7 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf krb5-multidev armhf 1.21.3-3 [126 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libaec0 armhf 1.1.3-1+b1 [21.9 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libsz2 armhf 1.1.3-1+b1 [8036 B] Get: 72 http://deb.debian.org/debian unstable/main armhf libaec-dev armhf 1.1.3-1+b1 [19.3 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf libbrotli-dev armhf 1.1.0-2+b6 [293 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libidn2-0 armhf 2.3.7-2+b1 [125 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libtasn1-6 armhf 4.19.0-3+b3 [43.9 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libgnutls30t64 armhf 3.8.8-2 [1370 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.19+dfsg-1 [163 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.6.0-2 [56.8 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.9.1-1 [115 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.9.1-1 [15.8 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 90 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.11.1-1 [311 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf libunbound8 armhf 1.22.0-1+b1 [539 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf libgnutls-dane0t64 armhf 3.8.8-2 [440 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf libgnutls-openssl27t64 armhf 3.8.8-2 [440 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf libp11-kit-dev armhf 0.25.5-3 [208 kB] Get: 97 http://deb.debian.org/debian unstable/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 98 http://deb.debian.org/debian unstable/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-3 [328 kB] Get: 99 http://deb.debian.org/debian unstable/main armhf libgmp-dev armhf 2:6.3.0+dfsg-3 [592 kB] Get: 100 http://deb.debian.org/debian unstable/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 101 http://deb.debian.org/debian unstable/main armhf libgnutls28-dev armhf 3.8.8-2 [1328 kB] Get: 102 http://deb.debian.org/debian unstable/main armhf libkrb5-dev armhf 1.21.3-3 [15.8 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf libldap-dev armhf 2.5.19+dfsg-1 [276 kB] Get: 104 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 105 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 106 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 107 http://deb.debian.org/debian unstable/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 108 http://deb.debian.org/debian unstable/main armhf libnghttp3-dev armhf 1.6.0-2 [81.8 kB] Get: 109 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls-dev armhf 1.9.1-1 [21.3 kB] Get: 110 http://deb.debian.org/debian unstable/main armhf libngtcp2-dev armhf 1.9.1-1 [165 kB] Get: 111 http://deb.debian.org/debian unstable/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 112 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 113 http://deb.debian.org/debian unstable/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 114 http://deb.debian.org/debian unstable/main armhf libssl-dev armhf 3.4.0-2 [2431 kB] Get: 115 http://deb.debian.org/debian unstable/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 116 http://deb.debian.org/debian unstable/main armhf libzstd-dev armhf 1.5.6+dfsg-2 [326 kB] Get: 117 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.11.1-1 [435 kB] Get: 118 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.11.1-1 [303 kB] Get: 119 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 120 http://deb.debian.org/debian unstable/main armhf libdeflate-dev armhf 1.22-1 [44.5 kB] Get: 121 http://deb.debian.org/debian unstable/main armhf libeigen3-dev all 3.4.0-4 [1041 kB] Get: 122 http://deb.debian.org/debian unstable/main armhf libhdf5-310 armhf 1.14.5+repack-3 [1272 kB] Get: 123 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-12 [263 kB] Get: 124 http://deb.debian.org/debian unstable/main armhf libhdf5-fortran-310 armhf 1.14.5+repack-3 [102 kB] Get: 125 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [67.3 kB] Get: 126 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-fortran-310 armhf 1.14.5+repack-3 [38.3 kB] Get: 127 http://deb.debian.org/debian unstable/main armhf libhdf5-cpp-310 armhf 1.14.5+repack-3 [125 kB] Get: 128 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-cpp-310 armhf 1.14.5+repack-3 [24.1 kB] Get: 129 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 130 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-3+b1 [263 kB] Get: 131 http://deb.debian.org/debian unstable/main armhf libjpeg-dev armhf 1:2.1.5-3+b1 [72.2 kB] Get: 132 http://deb.debian.org/debian unstable/main armhf libhdf5-dev armhf 1.14.5+repack-3 [3091 kB] Get: 133 http://deb.debian.org/debian unstable/main armhf libfast5-dev all 0.6.5-9 [49.1 kB] Get: 134 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB] Get: 135 http://deb.debian.org/debian unstable/main armhf libhts3t64 armhf 1.20+ds-2 [401 kB] Get: 136 http://deb.debian.org/debian unstable/main armhf liblzma-dev armhf 5.6.3-1+b1 [304 kB] Get: 137 http://deb.debian.org/debian unstable/main armhf libhts-dev armhf 1.20+ds-2 [1625 kB] Get: 138 http://deb.debian.org/debian unstable/main armhf libminimap2-dev armhf 2.27+dfsg-1+b2 [130 kB] Get: 139 http://deb.debian.org/debian unstable/main armhf libslow5-0t64 armhf 0.7.0+dfsg-3+b2 [57.9 kB] Get: 140 http://deb.debian.org/debian unstable/main armhf libslow5-dev armhf 0.7.0+dfsg-3+b2 [77.9 kB] Get: 141 http://deb.debian.org/debian unstable/main armhf libstreamvbyte0 armhf 0.4.1-4+b1 [5388 B] Get: 142 http://deb.debian.org/debian unstable/main armhf libstreamvbyte-dev armhf 0.4.1-4+b1 [6312 B] Fetched 52.0 MB in 1s (39.8 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:armhf. (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 ... 19561 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_armhf.deb ... Unpacking libpython3.13-minimal:armhf (3.13.1-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.1-3_armhf.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:armhf (3.13.1-3) ... Setting up libexpat1:armhf (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3) ... 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 ... 19895 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_armhf.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024b-5_all.deb ... Unpacking tzdata (2024b-5) ... Selecting previously unselected package libffi8:armhf. Preparing to unpack .../4-libffi8_3.4.6-1_armhf.deb ... Unpacking libffi8:armhf (3.4.6-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../6-libreadline8t64_8.2-6_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:armhf. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3_armhf.deb ... Unpacking libpython3.13-stdlib:armhf (3.13.1-3) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3_armhf.deb ... Unpacking python3.13 (3.13.1-3) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... 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 ... 20905 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_armhf.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.22.5-4_armhf.deb ... Unpacking gettext-base (0.22.5-4) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../006-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-7_armhf.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.40.2-14_armhf.deb ... Unpacking bsdextrautils (2.40.2-14) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../009-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../011-m4_1.4.19-5_armhf.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../012-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../013-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../014-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../015-autopoint_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../016-libcom-err2_1.47.2-1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.2-1) ... Selecting previously unselected package comerr-dev:armhf. Preparing to unpack .../017-comerr-dev_2.1-1.47.2-1_armhf.deb ... Unpacking comerr-dev:armhf (2.1-1.47.2-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../018-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../019-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../020-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../021-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../022-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../023-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../024-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../025-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libunistring5:armhf. Preparing to unpack .../026-libunistring5_1.3-1_armhf.deb ... Unpacking libunistring5:armhf (1.3-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../027-libicu72_72.1-6_armhf.deb ... Unpacking libicu72:armhf (72.1-6) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../028-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../029-gettext_0.22.5-4_armhf.deb ... Unpacking gettext (0.22.5-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../030-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../031-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../032-debhelper_13.23_all.deb ... Unpacking debhelper (13.23) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../033-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../034-python3-more-itertools_10.5.0-1_all.deb ... Unpacking python3-more-itertools (10.5.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../035-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../036-python3-typeguard_4.4.1-1_all.deb ... Unpacking python3-typeguard (4.4.1-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../037-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../038-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../039-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../040-python3-pkg-resources_75.6.0-1_all.deb ... Unpacking python3-pkg-resources (75.6.0-1) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../041-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../042-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../043-python3-setuptools_75.6.0-1_all.deb ... Unpacking python3-setuptools (75.6.0-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../044-dh-python_6.20250108_all.deb ... Unpacking dh-python (6.20250108) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../045-hdf5-helpers_1.14.5+repack-3_armhf.deb ... Unpacking hdf5-helpers (1.14.5+repack-3) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../046-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../047-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../048-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../049-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../050-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libgssrpc4t64:armhf. Preparing to unpack .../051-libgssrpc4t64_1.21.3-3_armhf.deb ... Unpacking libgssrpc4t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:armhf. Preparing to unpack .../052-libkadm5clnt-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5clnt-mit12:armhf (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:armhf. Preparing to unpack .../053-libkdb5-10t64_1.21.3-3_armhf.deb ... Unpacking libkdb5-10t64:armhf (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:armhf. Preparing to unpack .../054-libkadm5srv-mit12_1.21.3-3_armhf.deb ... Unpacking libkadm5srv-mit12:armhf (1.21.3-3) ... Selecting previously unselected package krb5-multidev:armhf. Preparing to unpack .../055-krb5-multidev_1.21.3-3_armhf.deb ... Unpacking krb5-multidev:armhf (1.21.3-3) ... Selecting previously unselected package libaec0:armhf. Preparing to unpack .../056-libaec0_1.1.3-1+b1_armhf.deb ... Unpacking libaec0:armhf (1.1.3-1+b1) ... Selecting previously unselected package libsz2:armhf. Preparing to unpack .../057-libsz2_1.1.3-1+b1_armhf.deb ... Unpacking libsz2:armhf (1.1.3-1+b1) ... Selecting previously unselected package libaec-dev:armhf. Preparing to unpack .../058-libaec-dev_1.1.3-1+b1_armhf.deb ... Unpacking libaec-dev:armhf (1.1.3-1+b1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../059-libbrotli1_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:armhf. Preparing to unpack .../060-libbrotli-dev_1.1.0-2+b6_armhf.deb ... Unpacking libbrotli-dev:armhf (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../061-libbz2-dev_1.0.8-6_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-6) ... Selecting previously unselected package libidn2-0:armhf. Preparing to unpack .../062-libidn2-0_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-0:armhf (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit0:armhf. Preparing to unpack .../063-libp11-kit0_0.25.5-3_armhf.deb ... Unpacking libp11-kit0:armhf (0.25.5-3) ... Selecting previously unselected package libtasn1-6:armhf. Preparing to unpack .../064-libtasn1-6_4.19.0-3+b3_armhf.deb ... Unpacking libtasn1-6:armhf (4.19.0-3+b3) ... Selecting previously unselected package libgnutls30t64:armhf. Preparing to unpack .../065-libgnutls30t64_3.8.8-2_armhf.deb ... Unpacking libgnutls30t64:armhf (3.8.8-2) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../066-libsasl2-modules-db_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../067-libsasl2-2_2.1.28+dfsg1-8_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../068-libldap-2.5-0_2.5.19+dfsg-1_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.19+dfsg-1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../069-libnghttp2-14_1.64.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:armhf. Preparing to unpack .../070-libnghttp3-9_1.6.0-2_armhf.deb ... Unpacking libnghttp3-9:armhf (1.6.0-2) ... Selecting previously unselected package libngtcp2-16:armhf. Preparing to unpack .../071-libngtcp2-16_1.9.1-1_armhf.deb ... Unpacking libngtcp2-16:armhf (1.9.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:armhf. Preparing to unpack .../072-libngtcp2-crypto-gnutls8_1.9.1-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls8:armhf (1.9.1-1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../073-libpsl5t64_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../074-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../075-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:armhf. Preparing to unpack .../076-libcurl3t64-gnutls_8.11.1-1_armhf.deb ... Unpacking libcurl3t64-gnutls:armhf (8.11.1-1) ... Selecting previously unselected package libevent-2.1-7t64:armhf. Preparing to unpack .../077-libevent-2.1-7t64_2.1.12-stable-10+b1_armhf.deb ... Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:armhf. Preparing to unpack .../078-libunbound8_1.22.0-1+b1_armhf.deb ... Unpacking libunbound8:armhf (1.22.0-1+b1) ... Selecting previously unselected package libgnutls-dane0t64:armhf. Preparing to unpack .../079-libgnutls-dane0t64_3.8.8-2_armhf.deb ... Unpacking libgnutls-dane0t64:armhf (3.8.8-2) ... Selecting previously unselected package libgnutls-openssl27t64:armhf. Preparing to unpack .../080-libgnutls-openssl27t64_3.8.8-2_armhf.deb ... Unpacking libgnutls-openssl27t64:armhf (3.8.8-2) ... Selecting previously unselected package libidn2-dev:armhf. Preparing to unpack .../081-libidn2-dev_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-dev:armhf (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:armhf. Preparing to unpack .../082-libp11-kit-dev_0.25.5-3_armhf.deb ... Unpacking libp11-kit-dev:armhf (0.25.5-3) ... Selecting previously unselected package libtasn1-6-dev:armhf. Preparing to unpack .../083-libtasn1-6-dev_4.19.0-3+b3_armhf.deb ... Unpacking libtasn1-6-dev:armhf (4.19.0-3+b3) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../084-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../085-libgmp-dev_2%3a6.3.0+dfsg-3_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-3) ... Selecting previously unselected package nettle-dev:armhf. Preparing to unpack .../086-nettle-dev_3.10-1+b1_armhf.deb ... Unpacking nettle-dev:armhf (3.10-1+b1) ... Selecting previously unselected package libgnutls28-dev:armhf. Preparing to unpack .../087-libgnutls28-dev_3.8.8-2_armhf.deb ... Unpacking libgnutls28-dev:armhf (3.8.8-2) ... Selecting previously unselected package libkrb5-dev:armhf. Preparing to unpack .../088-libkrb5-dev_1.21.3-3_armhf.deb ... Unpacking libkrb5-dev:armhf (1.21.3-3) ... Selecting previously unselected package libldap-dev:armhf. Preparing to unpack .../089-libldap-dev_2.5.19+dfsg-1_armhf.deb ... Unpacking libldap-dev:armhf (2.5.19+dfsg-1) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../090-libpkgconf3_1.8.1-4_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../091-pkgconf-bin_1.8.1-4_armhf.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../092-pkgconf_1.8.1-4_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:armhf. Preparing to unpack .../093-libnghttp2-dev_1.64.0-1_armhf.deb ... Unpacking libnghttp2-dev:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:armhf. Preparing to unpack .../094-libnghttp3-dev_1.6.0-2_armhf.deb ... Unpacking libnghttp3-dev:armhf (1.6.0-2) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:armhf. Preparing to unpack .../095-libngtcp2-crypto-gnutls-dev_1.9.1-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls-dev:armhf (1.9.1-1) ... Selecting previously unselected package libngtcp2-dev:armhf. Preparing to unpack .../096-libngtcp2-dev_1.9.1-1_armhf.deb ... Unpacking libngtcp2-dev:armhf (1.9.1-1) ... Selecting previously unselected package libpsl-dev:armhf. Preparing to unpack .../097-libpsl-dev_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl-dev:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../098-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:armhf. Preparing to unpack .../099-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../100-libssl-dev_3.4.0-2_armhf.deb ... Unpacking libssl-dev:armhf (3.4.0-2) ... Selecting previously unselected package libssh2-1-dev:armhf. Preparing to unpack .../101-libssh2-1-dev_1.11.1-1_armhf.deb ... Unpacking libssh2-1-dev:armhf (1.11.1-1) ... Selecting previously unselected package libzstd-dev:armhf. Preparing to unpack .../102-libzstd-dev_1.5.6+dfsg-2_armhf.deb ... Unpacking libzstd-dev:armhf (1.5.6+dfsg-2) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../103-libcurl4-gnutls-dev_8.11.1-1_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (8.11.1-1) ... Selecting previously unselected package libcurl4t64:armhf. Preparing to unpack .../104-libcurl4t64_8.11.1-1_armhf.deb ... Unpacking libcurl4t64:armhf (8.11.1-1) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../105-libdeflate0_1.22-1_armhf.deb ... Unpacking libdeflate0:armhf (1.22-1) ... Selecting previously unselected package libdeflate-dev:armhf. Preparing to unpack .../106-libdeflate-dev_1.22-1_armhf.deb ... Unpacking libdeflate-dev:armhf (1.22-1) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../107-libeigen3-dev_3.4.0-4_all.deb ... Unpacking libeigen3-dev (3.4.0-4) ... Selecting previously unselected package libhdf5-310:armhf. Preparing to unpack .../108-libhdf5-310_1.14.5+repack-3_armhf.deb ... Unpacking libhdf5-310:armhf (1.14.5+repack-3) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../109-libgfortran5_14.2.0-12_armhf.deb ... Unpacking libgfortran5:armhf (14.2.0-12) ... Selecting previously unselected package libhdf5-fortran-310:armhf. Preparing to unpack .../110-libhdf5-fortran-310_1.14.5+repack-3_armhf.deb ... Unpacking libhdf5-fortran-310:armhf (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-310:armhf. Preparing to unpack .../111-libhdf5-hl-310_1.14.5+repack-3_armhf.deb ... Unpacking libhdf5-hl-310:armhf (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-fortran-310:armhf. Preparing to unpack .../112-libhdf5-hl-fortran-310_1.14.5+repack-3_armhf.deb ... Unpacking libhdf5-hl-fortran-310:armhf (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-cpp-310:armhf. Preparing to unpack .../113-libhdf5-cpp-310_1.14.5+repack-3_armhf.deb ... Unpacking libhdf5-cpp-310:armhf (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-cpp-310:armhf. Preparing to unpack .../114-libhdf5-hl-cpp-310_1.14.5+repack-3_armhf.deb ... Unpacking libhdf5-hl-cpp-310:armhf (1.14.5+repack-3) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../115-libjpeg62-turbo_1%3a2.1.5-3+b1_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Selecting previously unselected package libjpeg62-turbo-dev:armhf. Preparing to unpack .../116-libjpeg62-turbo-dev_1%3a2.1.5-3+b1_armhf.deb ... Unpacking libjpeg62-turbo-dev:armhf (1:2.1.5-3+b1) ... Selecting previously unselected package libjpeg-dev:armhf. Preparing to unpack .../117-libjpeg-dev_1%3a2.1.5-3+b1_armhf.deb ... Unpacking libjpeg-dev:armhf (1:2.1.5-3+b1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../118-libhdf5-dev_1.14.5+repack-3_armhf.deb ... Unpacking libhdf5-dev (1.14.5+repack-3) ... Selecting previously unselected package libfast5-dev. Preparing to unpack .../119-libfast5-dev_0.6.5-9_all.deb ... Unpacking libfast5-dev (0.6.5-9) ... Selecting previously unselected package libhtscodecs2:armhf. Preparing to unpack .../120-libhtscodecs2_1.6.1-1_armhf.deb ... Unpacking libhtscodecs2:armhf (1.6.1-1) ... Selecting previously unselected package libhts3t64:armhf. Preparing to unpack .../121-libhts3t64_1.20+ds-2_armhf.deb ... Unpacking libhts3t64:armhf (1.20+ds-2) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../122-liblzma-dev_5.6.3-1+b1_armhf.deb ... Unpacking liblzma-dev:armhf (5.6.3-1+b1) ... Selecting previously unselected package libhts-dev:armhf. Preparing to unpack .../123-libhts-dev_1.20+ds-2_armhf.deb ... Unpacking libhts-dev:armhf (1.20+ds-2) ... Selecting previously unselected package libminimap2-dev. Preparing to unpack .../124-libminimap2-dev_2.27+dfsg-1+b2_armhf.deb ... Unpacking libminimap2-dev (2.27+dfsg-1+b2) ... Selecting previously unselected package libslow5-0t64:armhf. Preparing to unpack .../125-libslow5-0t64_0.7.0+dfsg-3+b2_armhf.deb ... Unpacking libslow5-0t64:armhf (0.7.0+dfsg-3+b2) ... Selecting previously unselected package libslow5-dev:armhf. Preparing to unpack .../126-libslow5-dev_0.7.0+dfsg-3+b2_armhf.deb ... Unpacking libslow5-dev:armhf (0.7.0+dfsg-3+b2) ... Selecting previously unselected package libstreamvbyte0:armhf. Preparing to unpack .../127-libstreamvbyte0_0.4.1-4+b1_armhf.deb ... Unpacking libstreamvbyte0:armhf (0.4.1-4+b1) ... Selecting previously unselected package libstreamvbyte-dev:armhf. Preparing to unpack .../128-libstreamvbyte-dev_0.4.1-4+b1_armhf.deb ... Unpacking libstreamvbyte-dev:armhf (0.4.1-4+b1) ... Setting up libhtscodecs2:armhf (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libstreamvbyte0:armhf (0.4.1-4+b1) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libicu72:armhf (72.1-6) ... Setting up libzstd-dev:armhf (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.2-14) ... Setting up hdf5-helpers (1.14.5+repack-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-4) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Setting up libcom-err2:armhf (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:armhf (1.1.3-1+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jan 9 13:43:34 UTC 2025. Universal Time is now: Thu Jan 9 13:43:34 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libunbound8:armhf (1.22.0-1+b1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up libgmpxx4ldbl:armhf (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-3+b1) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-3+b1) ... Setting up libstreamvbyte-dev:armhf (0.4.1-4+b1) ... Setting up comerr-dev:armhf (2.1-1.47.2-1) ... Setting up libunistring5:armhf (1.3-1) ... Setting up libssl-dev:armhf (3.4.0-2) ... Setting up autopoint (0.22.5-4) ... Setting up libslow5-0t64:armhf (0.7.0+dfsg-3+b2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up libgfortran5:armhf (14.2.0-12) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:armhf (1.6.0-2) ... Setting up libnghttp3-dev:armhf (1.6.0-2) ... Setting up liblzma-dev:armhf (5.6.3-1+b1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:armhf (3.4.6-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libtasn1-6:armhf (4.19.0-3+b3) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:armhf (1.9.1-1) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libtasn1-6-dev:armhf (4.19.0-3+b3) ... Setting up libdeflate-dev:armhf (1.22-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:armhf (1.1.0-2+b6) ... Setting up libsz2:armhf (1.1.3-1+b1) ... Setting up libbz2-dev:armhf (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-4) ... Setting up libgmp-dev:armhf (2:6.3.0+dfsg-3) ... Setting up nettle-dev:armhf (3.10-1+b1) ... Setting up libtool (2.5.4-2) ... Setting up libaec-dev:armhf (1.1.3-1+b1) ... Setting up libjpeg-dev:armhf (1:2.1.5-3+b1) ... Setting up libidn2-0:armhf (2.3.7-2+b1) ... Setting up libslow5-dev:armhf (0.7.0+dfsg-3+b2) ... Setting up libngtcp2-dev:armhf (1.9.1-1) ... Setting up pkgconf:armhf (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libminimap2-dev (2.27+dfsg-1+b2) ... Setting up libp11-kit0:armhf (0.25.5-3) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libssh2-1-dev:armhf (1.11.1-1) ... Setting up libidn2-dev:armhf (2.3.7-2+b1) ... Setting up libreadline8t64:armhf (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:armhf (3.13.1-3) ... Setting up libp11-kit-dev:armhf (0.25.5-3) ... Setting up libpython3-stdlib:armhf (3.13.1-2) ... Setting up libgnutls30t64:armhf (3.8.8-2) ... Setting up libgnutls-openssl27t64:armhf (3.8.8-2) ... Setting up libnghttp2-dev:armhf (1.64.0-1) ... Setting up python3.13 (3.13.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:armhf (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 libldap-2.5-0:armhf (2.5.19+dfsg-1) ... Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:armhf (3.8.8-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:armhf (1.21.3-3) ... Setting up libldap-dev:armhf (2.5.19+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libngtcp2-crypto-gnutls8:armhf (1.9.1-1) ... Setting up libkadm5clnt-mit12:armhf (1.21.3-3) ... Setting up libgnutls28-dev:armhf (3.8.8-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:armhf (8.11.1-1) ... Setting up libkdb5-10t64:armhf (1.21.3-3) ... Setting up python3-typeguard (4.4.1-1) ... Setting up libcurl3t64-gnutls:armhf (8.11.1-1) ... Setting up debhelper (13.23) ... Setting up libngtcp2-crypto-gnutls-dev:armhf (1.9.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-310:armhf (1.14.5+repack-3) ... Setting up libkadm5srv-mit12:armhf (1.21.3-3) ... Setting up libhts3t64:armhf (1.20+ds-2) ... Setting up libhdf5-fortran-310:armhf (1.14.5+repack-3) ... Setting up krb5-multidev:armhf (1.21.3-3) ... Setting up libhdf5-cpp-310:armhf (1.14.5+repack-3) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up libhdf5-hl-310:armhf (1.14.5+repack-3) ... Setting up python3-setuptools (75.6.0-1) ... Setting up libkrb5-dev:armhf (1.21.3-3) ... Setting up dh-python (6.20250108) ... Setting up libhdf5-hl-cpp-310:armhf (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:armhf (1.14.5+repack-3) ... Setting up libcurl4-gnutls-dev:armhf (8.11.1-1) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libhts-dev:armhf (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: user script /srv/workspace/pbuilder/30279/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/30279/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/nanopolish-0.14.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 armhf 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 -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' rm -f ./.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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_alignment_db.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/basemods/nanopolish_basemods.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_detect_polyi.cpp src/nanopolish_fast5_check.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend; g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 src/common/nanopolish_variant.cpp: In function 'void score_variant_group(VariantGroup&, Haplotype, const std::vector&, int, int, bool, uint32_t, const std::vector >&)': src/common/nanopolish_variant.cpp:210:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 210 | fprintf(stderr, "Number of variants in span (%lu) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes!\n", num_variants); | ~~^ ~~~~~~~~~~~~ | | | | long unsigned int size_t {aka unsigned int} | %u 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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 src/io/nanopolish_fast5_loader.cpp: In static member function 'static Fast5Data Fast5Loader::load_read(slow5_file_t*, const std::string&)': src/io/nanopolish_fast5_loader.cpp:94:34: warning: narrowing conversion of 'rec->slow5_rec::len_raw_signal' from 'uint64_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 94 | data.rt = (raw_table) { rec->len_raw_signal, 0, rec->len_raw_signal, rawptr }; | ~~~~~^~~~~~~~~~~~~~ src/io/nanopolish_fast5_loader.cpp:94:58: warning: narrowing conversion of 'rec->slow5_rec::len_raw_signal' from 'uint64_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 94 | data.rt = (raw_table) { rec->len_raw_signal, 0, rec->len_raw_signal, rawptr }; | ~~~~~^~~~~~~~~~~~~~ src/io/nanopolish_fast5_io.cpp: In function 'raw_table fast5_get_raw_samples(fast5_file&, const std::string&, fast5_raw_scaling)': src/io/nanopolish_fast5_io.cpp:162:28: warning: narrowing conversion of 'nsample' from 'hsize_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 162 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr }; | ^~~~~~~ src/io/nanopolish_fast5_io.cpp:162:40: warning: narrowing conversion of 'nsample' from 'hsize_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 162 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr }; | ^~~~~~~ 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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_fast5_check.cpp src/nanopolish_call_variants.cpp: In function 'Haplotype fix_homopolymers(const Haplotype&, const AlignmentDB&)': src/nanopolish_call_variants.cpp:680:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 680 | fprintf(stderr, "SUM_VAR\t%zu\t%zu\t%d\t%d\t%lu\t%.5lf\t%.2lf\n", ref_hp_start, hp_length, var_sequence_length, call_window, variant_offset_end - variant_offset_start, sum_duration, log_gamma); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int size_t {aka unsigned int} | %u 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 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 | %lld 1041 | read_name.c_str(), ref_name.c_str(), record->core.pos); | ~~~~~~~~~~~~~~~~ | | | long long int src/nanopolish_detect_polyi.cpp:1105:35: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long 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 | %lld 1106 | read_name.c_str(), ref_name.c_str(), record->core.pos, | ~~~~~~~~~~~~~~~~ | | | long long int 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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 src/nanopolish_haplotype.cpp: In member function 'void Haplotype::print_debug_info() const': src/nanopolish_haplotype.cpp:172:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=] 172 | fprintf(stderr, "[haplotype-debug] ctg: %s, position: %lu\n", m_ref_name.c_str(), m_ref_position); | ~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int unsigned int | %u 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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_polya_estimator.cpp src/nanopolish_index.cpp: In function 'int index_main(int, char**)': src/nanopolish_index.cpp:386:72: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 386 | fprintf(stderr,"fast5 files could not be located for %ld reads\n",num_reads-num_with_path); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d 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 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 | %lld 766 | read_name.c_str(), ref_name.c_str(), record->core.pos); | ~~~~~~~~~~~~~~~~ | | | long long int src/nanopolish_polya_estimator.cpp:823:35: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long 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 | %lld 824 | read_name.c_str(), ref_name.c_str(), record->core.pos, | ~~~~~~~~~~~~~~~~ | | | long long int 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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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/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 -O3 -flto -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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/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 -O3 -flto -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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/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 -O3 -flto -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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/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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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/arm-linux-gnueabihf/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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_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/arm-linux-gnueabihf/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: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: debian/nanopolish/usr/lib/nanopolish/nanopolish_test contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin dpkg-shlibdeps: warning: debian/nanopolish/usr/bin/nanopolish contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin 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-dbgsym' in '../nanopolish-dbgsym_0.14.0-1_armhf.deb'. dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../nanopolish_0.14.0-1_armhf.buildinfo dpkg-genchanges --build=binary -O../nanopolish_0.14.0-1_armhf.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: user script /srv/workspace/pbuilder/30279/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/30279/tmp/hooks/B01_cleanup finished 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/30279 and its subdirectories I: Current time: Fri Jan 10 03:48:12 +14 2025 I: pbuilder-time-stamp: 1736430492