Tue Apr 9 07:52:19 UTC 2024 I: starting to build nanopolish/unstable/i386 on jenkins on '2024-04-09 07:52' Tue Apr 9 07:52:19 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_11/6754/console.log Tue Apr 9 07:52:19 UTC 2024 I: Downloading source for unstable/nanopolish=0.14.0-1 --2024-04-09 07:52:19-- http://deb.debian.org/debian/pool/main/n/nanopolish/nanopolish_0.14.0-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2114 (2.1K) [text/prs.lines.tag] Saving to: ‘nanopolish_0.14.0-1.dsc’ 0K .. 100% 195M=0s 2024-04-09 07:52:19 (195 MB/s) - ‘nanopolish_0.14.0-1.dsc’ saved [2114/2114] Tue Apr 9 07:52:19 UTC 2024 I: nanopolish_0.14.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: nanopolish Binary: nanopolish Architecture: any Version: 0.14.0-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/jts/nanopolish Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/nanopolish Vcs-Git: https://salsa.debian.org/med-team/nanopolish.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev Package-List: nanopolish deb science optional arch=any Checksums-Sha1: a26c2a1a0f41a0e3fef52dee3d6ef1aea11e0266 4073583 nanopolish_0.14.0.orig.tar.gz 70b1db592822052179b1c679ea8999f0af4c5e94 8976 nanopolish_0.14.0-1.debian.tar.xz Checksums-Sha256: bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78 4073583 nanopolish_0.14.0.orig.tar.gz 6c5a39be2682ee430fcc2daf99c7574adf9f0110d4caa13f29af767a995d5bfe 8976 nanopolish_0.14.0-1.debian.tar.xz Files: 90b445d40348427fd009bea3e04f0249 4073583 nanopolish_0.14.0.orig.tar.gz f33e6f1fb88a7cbe9d018781b5d2758c 8976 nanopolish_0.14.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmLJxmwSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxQFgP/09lwg+fdXMZDQIP7yO14o6+RPrMa9xP v4Ujack8J7iodJ3mqRiDEgggiQFyMjJHs2Qu/25pi0QBhXArcf0RD6UwTmjfURIi gecCqIfCtQieRsBa7m2gNdqIQ8a4DDHEmyQzg7xLSPl/clRHyWSK/KTLM2tfly1E hsW6orjxEDjvewy4xfc/LYp5vBDZuBQR+mOii5NDGdAhNxCgbxeP5inlN9cdu4hu 2RGvgdpuF8Z2/dK6iGZJeNIiB6MRNpcPLvVn+tjnxpon+ejhTISWQzNj5/saur3x PO/mHZLJCpfrHY2aXGL+nQr7Em0584uLZFH0YTCHBwlBBxhntgND9bHyhT6BbFdN MVAJTiIdYyH8krbOLSRv/KhDrbqcB03T5kxvUpvtB26GMiTtApoBFhikwLc8E8bd 9VzzRe2g9zaDZpd829n8ebjR0WfJDxpQV0JDe6X9r+KPVzvwCrO3fFc7/k2kcqIm O7xhU+28qbd29TbVWLlusXOczkJYbVKCDOCy860LXp4rrZ5O+5bpvNcTHIJOA3d9 HXIe4NwJRTvf/d52Ax/rG6GRZ8KVpjdRptVuUEudMAbuFkqidFz3cVaEN658xxEN VhXxVMi688dIYZYxcKq+7BNr6X79JXo6uUHzgaxT0+ueYe2oq4my+cxfAxtIo6vq 4aSdl//rZLAg =W3aC -----END PGP SIGNATURE----- Tue Apr 9 07:52:19 UTC 2024 I: Checking whether the package is not for us Tue Apr 9 07:52:19 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Tue Apr 9 07:52:19 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Tue Apr 9 07:54:13 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 12 02:15:18 -12 2025 I: pbuilder-time-stamp: 1747059318 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: using eatmydata during job 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 gpgv: Signature made Sat Jul 9 18:18:20 2022 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./nanopolish_0.14.0-1.dsc: no acceptable signature found 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/125075/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='d1ca50b7bca143f1b0f3b91e0f7a27ab' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='125075' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.zLteyVLm/pbuilderrc_U5UL --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zLteyVLm/b1 --logfile b1/build.log nanopolish_0.14.0-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos6-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/125075/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: i386 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 ... 19682 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} 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} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libbrotli1{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} libexpat1{a} libfast5-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libminimap2-dev{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libslow5-0t64{a} libslow5-dev{a} libssh2-1t64{a} libssl-dev{a} libstreamvbyte-dev{a} libstreamvbyte0{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 99 newly installed, 0 to remove and 0 not upgraded. Need to get 42.8 MB of archives. After unpacking 166 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.11-minimal i386 3.11.8-3+b3 [816 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.11-minimal i386 3.11.8-3+b3 [1917 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024a-2 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libpython3.11-stdlib i386 3.11.8-3+b3 [1793 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 python3.11 i386 3.11.8-3+b3 [597 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.11.8-1 [9336 B] Get: 13 http://deb.debian.org/debian unstable/main i386 python3 i386 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40-5 [96.7 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 python3-lib2to3 all 3.12.2-3 [77.6 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 python3-distutils all 3.12.2-3 [131 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 68.1.2-2 [468 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20240401 [107 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 hdf5-helpers i386 1.10.10+repack-3.3 [23.4 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libaec0 i386 1.1.3-1 [24.5 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 libsz2 i386 1.1.3-1 [7824 B] Get: 52 http://deb.debian.org/debian unstable/main i386 libaec-dev i386 1.1.3-1 [22.4 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.0-2.4 [20.6 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.20.1-6+b1 [36.1 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.20.1-6+b1 [83.2 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] Get: 58 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.20.1-6+b1 [360 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.20.1-6+b1 [145 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-6 [20.5 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-6 [60.6 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.16+dfsg-2 [198 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.61.0-1 [83.7 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.0-4.1+b2 [225 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.7.1-2 [467 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libcurl4-gnutls-dev i386 8.7.1-2 [589 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.7.1-2 [477 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libdeflate-dev i386 1.20-1 [56.0 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-1+b2 [38.5 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-1+b2 [30.2 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-1+b2 [26.2 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 pkg-config i386 1.8.1-1+b2 [14.0 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libhdf5-103-1t64 i386 1.10.10+repack-3.3 [1178 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14-20240330-1 [735 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libhdf5-fortran-102t64 i386 1.10.10+repack-3.3 [98.2 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-100t64 i386 1.10.10+repack-3.3 [74.4 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-fortran-100t64 i386 1.10.10+repack-3.3 [41.8 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libhdf5-cpp-103-1t64 i386 1.10.10+repack-3.3 [138 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-cpp-100t64 i386 1.10.10+repack-3.3 [21.8 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo-dev i386 1:2.1.5-2+b2 [303 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libjpeg-dev i386 1:2.1.5-2+b2 [72.1 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libssl-dev i386 3.2.1-3 [2744 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libhdf5-dev i386 1.10.10+repack-3.3 [2772 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libfast5-dev all 0.6.5-7 [50.2 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.19+ds-1.1+b1 [491 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 liblzma-dev i386 5.6.1+really5.4.5-1 [304 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libhts-dev i386 1.19+ds-1.1+b1 [1660 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libminimap2-dev i386 2.27+dfsg-1 [139 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libslow5-0t64 i386 0.7.0+dfsg-2.1 [61.7 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libslow5-dev i386 0.7.0+dfsg-2.1 [83.3 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libstreamvbyte0 i386 0.4.1-4 [5888 B] Get: 99 http://deb.debian.org/debian unstable/main i386 libstreamvbyte-dev i386 0.4.1-4 [6576 B] Fetched 42.8 MB in 1s (53.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19682 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-3+b3_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-3+b3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.2-1_i386.deb ... Unpacking libexpat1:i386 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. 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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.8-3+b3_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.8-3+b3) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.8-3+b3_i386.deb ... Unpacking python3.11 (3.11.8-3+b3) ... Selecting previously unselected package libpython3-stdlib:i386. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/nanopolish-0.14.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../nanopolish_0.14.0-1_source.changes dpkg-buildpackage: info: source package nanopolish dpkg-buildpackage: info: source version 0.14.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 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 -j22 "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 -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/main/nanopolish.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/basemods/nanopolish_basemods.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_detect_polyi.cpp src/nanopolish_fast5_check.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend; g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_alignment_db.cpp g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_anchor.cpp g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_eventalign.cpp g++ -o src/basemods/nanopolish_basemods.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/basemods/nanopolish_basemods.cpp g++ -o src/common/fs_support.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/fs_support.cpp g++ -o src/common/logsum.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/logsum.cpp g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_alphabet.cpp g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_bam_processor.cpp g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_bam_utils.cpp g++ -o src/common/nanopolish_common.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_common.cpp g++ -o src/common/nanopolish_iupac.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_iupac.cpp g++ -o src/common/nanopolish_klcs.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_klcs.cpp g++ -o src/common/nanopolish_variant.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_variant.cpp g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_duration_model.cpp g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm.cpp g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_transition_parameters.cpp g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_io.cpp g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_loader.cpp g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_processor.cpp g++ -o src/nanopolish_call_methylation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_call_methylation.cpp g++ -o src/nanopolish_call_variants.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_call_variants.cpp g++ -o src/nanopolish_detect_polyi.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_detect_polyi.cpp 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 }; | ~~~~~^~~~~~~~~~~~~~ g++ -o src/nanopolish_fast5_check.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_fast5_check.cpp src/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_haplotype.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_haplotype.cpp g++ -o src/nanopolish_index.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_index.cpp g++ -o src/nanopolish_methyltrain.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_methyltrain.cpp g++ -o src/nanopolish_phase_reads.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_phase_reads.cpp g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_polya_estimator.cpp g++ -o src/nanopolish_raw_loader.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_raw_loader.cpp g++ -o src/nanopolish_read_db.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_read_db.cpp 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/nanopolish_scorereads.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_scorereads.cpp g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_squiggle_read.cpp g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp g++ -o src/nanopolish_variant_db.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_variant_db.cpp 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_vcf2fasta.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_vcf2fasta.cpp g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_model_names.cpp 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 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 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 -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_pore_model_set.cpp g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_poremodel.cpp 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 g++ -o src/training_core.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/training_core.cpp cc -o src/thirdparty/fet.o -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/thirdparty/fet.c 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 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 -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/thirdparty/scrappie/event_detection.c cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/thirdparty/scrappie/scrappie_common.c cc -o src/thirdparty/stdaln.o -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/thirdparty/stdaln.c g++ -o nanopolish -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_fast5_check.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -lslow5 -lstreamvbyte -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial lto-wrapper: warning: using serial compilation of 10 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information 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 -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/test/nanopolish_test.cpp g++ -o nanopolish_test -g -O2 -ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_fast5_check.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -lslow5 -lstreamvbyte -Wl,-z,relro -Wl,-z,now -L/usr/lib/i386-linux-gnu/hdf5/serial lto-wrapper: warning: using serial compilation of 7 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information make[2]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' make[1]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' echo "Since we need the executable created inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck." Since we need the executable created inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck. make[1]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/nanopolish/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' dh_install for pl in `find debian -name "*.pl"` ; do \ sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' ${pl} ; \ done for pl in `grep -Rl '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \ sed -i '1s?^#!.*python.*?#!/usr/bin/python3?' ${pl} ; \ done make[1]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/nanopolish-0.14.0' dh_fixperms find debian -name *.fast5 -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/nanopolish-0.14.0' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: 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_i386.deb'. dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../nanopolish_0.14.0-1_i386.buildinfo dpkg-genchanges --build=binary -O../nanopolish_0.14.0-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/125075 and its subdirectories I: Current time: Mon May 12 02:17:10 -12 2025 I: pbuilder-time-stamp: 1747059430 Tue Apr 9 07:54:13 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Tue Apr 9 07:54:13 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Tue Apr 9 07:59:00 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Tue Apr 9 07:59:01 UTC 2024 I: nanopolish_0.14.0-1_i386.changes: Format: 1.8 Date: Sat, 09 Jul 2022 23:37:52 +0530 Source: nanopolish Binary: nanopolish nanopolish-dbgsym Architecture: i386 Version: 0.14.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: nanopolish - consensus caller for nanopore sequencing data Changes: nanopolish (0.14.0-1) unstable; urgency=medium . * Team Upload. . [ Andreas Tille ] * New upstream version * Standards-Version: 4.6.1 (routine-update) . [ Nilesh Patra ] * Add opt to link against external slow5lib * B-D on libslow5lib * d/rules: export SLOW5LIB=external Checksums-Sha1: 426245f48f936e867d3f7afff5bbcd05812096d9 7542736 nanopolish-dbgsym_0.14.0-1_i386.deb 097d9a87201bd0ee1f30ab7c72fe084ce3a0d803 7595 nanopolish_0.14.0-1_i386.buildinfo 536b6d62d80f5230295f9329ab2dc3b6c62f56d4 2219344 nanopolish_0.14.0-1_i386.deb Checksums-Sha256: 734bcf06c7c1ca7a3d4f17dc7a4bcf137bb3c3b3dcb251dc0fc5ad673516ca99 7542736 nanopolish-dbgsym_0.14.0-1_i386.deb 9119411fec09af118933c4898e008196d65e45ca69359c59ae80a3c0cd88fa00 7595 nanopolish_0.14.0-1_i386.buildinfo fdb584ece7d91a482af9a584becc92b5458d1fd5a1b1ec85dc268f6671fa8ece 2219344 nanopolish_0.14.0-1_i386.deb Files: 4353b4688e8c7a10ae8eb84bf8e182a8 7542736 debug optional nanopolish-dbgsym_0.14.0-1_i386.deb c74e7f591dd67d683f8ed8c1b3bfe1b7 7595 science optional nanopolish_0.14.0-1_i386.buildinfo 680374beb7549d5782f49b640a3c9097 2219344 science optional nanopolish_0.14.0-1_i386.deb Tue Apr 9 07:59:02 UTC 2024 I: diffoscope 263 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_11-6754.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.zLteyVLm/nanopolish_0.14.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.zLteyVLm/nanopolish_0.14.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.zLteyVLm/nanopolish_0.14.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.zLteyVLm/b1/nanopolish_0.14.0-1_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.zLteyVLm/b2/nanopolish_0.14.0-1_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.486s) 0.486s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.122s) 0.122s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 845ms CPU time consumed: 842ms Tue Apr 9 07:59:03 UTC 2024 I: diffoscope 263 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 9 07:59:03 UTC 2024 I: nanopolish from unstable built successfully and reproducibly on i386. Tue Apr 9 07:59:05 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 9 07:59:05 UTC 2024 I: Submitting 12K b1/nanopolish_0.14.0-1_i386.buildinfo.asc Tue Apr 9 07:59:07 UTC 2024 I: Submitting 12K b2/nanopolish_0.14.0-1_i386.buildinfo.asc Tue Apr 9 07:59:07 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 9 07:59:07 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 9 07:59:08 UTC 2024 I: Removing signed nanopolish_0.14.0-1_i386.buildinfo.asc files: removed './b1/nanopolish_0.14.0-1_i386.buildinfo.asc' removed './b2/nanopolish_0.14.0-1_i386.buildinfo.asc'