Thu Nov 28 04:59:39 UTC 2024 I: starting to build obitools/trixie/armhf on jenkins on '2024-11-28 04:59' Thu Nov 28 04:59:39 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_18/8549/console.log Thu Nov 28 04:59:39 UTC 2024 I: Downloading source for trixie/obitools=3.0.1~b26+dfsg-3 --2024-11-28 04:59:39-- http://deb.debian.org/debian/pool/main/o/obitools/obitools_3.0.1%7eb26%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2210 (2.2K) [text/prs.lines.tag] Saving to: ‘obitools_3.0.1~b26+dfsg-3.dsc’ 0K .. 100% 349M=0s 2024-11-28 04:59:39 (349 MB/s) - ‘obitools_3.0.1~b26+dfsg-3.dsc’ saved [2210/2210] Thu Nov 28 04:59:39 UTC 2024 I: obitools_3.0.1~b26+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: obitools Binary: obitools Architecture: any Version: 3.0.1~b26+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille Homepage: https://metabarcoding.org/obitools3 Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/obitools Vcs-Git: https://salsa.debian.org/med-team/obitools.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: less Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-dev:native, libpython3-dev, python3-setuptools, cython3, cmake Package-List: obitools deb science optional arch=any Checksums-Sha1: 79040b3e48957ae1669e2b094fb3fc56a8d0db7b 255092 obitools_3.0.1~b26+dfsg.orig.tar.xz 880f7d3e5ed3a90e154997172fe470728ad2057d 3556832 obitools_3.0.1~b26+dfsg-3.debian.tar.xz Checksums-Sha256: 6f067e22b76e4489288f7a3d13027391ecba5719de324c2ca58ec4542bc60e91 255092 obitools_3.0.1~b26+dfsg.orig.tar.xz 0b79fc02688c6b6bc60ac9d8e5415f91fdf750ae4b1c5a0b6fd2b00bb5218ca5 3556832 obitools_3.0.1~b26+dfsg-3.debian.tar.xz Files: 974e65eaa6d1a2f51a7f5594b6987349 255092 obitools_3.0.1~b26+dfsg.orig.tar.xz 3036039d013d939b2e214e8912c188c1 3556832 obitools_3.0.1~b26+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmc/VXASHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+bi42EP/2QKQ98tQuiecGBFQt9elCmKAEVThZ5D yJ7sWoKMg+5zozDEJdYwt9P7rrht1ziSBD/rX+s9ukDuk2PulRfHD0k/x2PvRzA5 IHe6J/34yGwiEzxK2vBdnWNzCVQpeGS3Cs83/UAK0pnkIr6l17/k4TS04CjHYKfB XXWW05LV2UFH13EqZuRWN4mKgOhLYhUOSoBdLDqBDuV+0KnTL4eWbVxGUAY/Y7pd XfJ02xy8Dz3oJMnmU4tYH3M0Lf6GX9EYxrQcQCNc1twE6T5vOZ2/WLuMh78J67V7 S07nBIFf2LZ34DQLLxnhPARElzro/3XTphqNwra/1SqZ3ROeTh6IuigofJUEyE6d R7wwjV5/j1QvAXPlu2tAuZ8vRPpj7Y+3o5Uz4HTe5G4ixzYtVFQ57mYdxO2v+OEu v4MvX1RusNab/+WRhiUMd9lFBEkZeK1mzNcteizsQDUAbvYuQ8dovPzHrSeozinB fxx8EeU2jlkjGblsrED9qd7ypMity65hiWFjT0zmIymGNVKmg5u8eUFyrGrw82cX lmGBwKzHgUX44lCOEV7Dv1bR3pfYnAe/QAEE6NVJiJ6QoSMNsQPq86i8+ke+qNYl hd38rYvPOBBEEly0RVqRaa2RecnCw5qFvgK9weNH82zusheUgqRwoLCxeAcVPoyS zrfSmG4kgCSV =vPIl -----END PGP SIGNATURE----- Thu Nov 28 04:59:39 UTC 2024 I: Checking whether the package is not for us Thu Nov 28 04:59:39 UTC 2024 I: Starting 1st build on remote node ff64a-armhf-rb.debian.net. Thu Nov 28 04:59:39 UTC 2024 I: Preparing to do remote build '1' on ff64a-armhf-rb.debian.net. Thu Nov 28 05:36:25 UTC 2024 I: Deleting $TMPDIR on ff64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 27 16:59:47 -12 2024 I: pbuilder-time-stamp: 1732769987 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [obitools_3.0.1~b26+dfsg-3.dsc] I: copying [./obitools_3.0.1~b26+dfsg.orig.tar.xz] I: copying [./obitools_3.0.1~b26+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Nov 21 15:44:48 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: issuer "crusoe@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./obitools_3.0.1~b26+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting obitools in obitools-3.0.1~b26+dfsg dpkg-source: info: unpacking obitools_3.0.1~b26+dfsg.orig.tar.xz dpkg-source: info: unpacking obitools_3.0.1~b26+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cmake_debian_options dpkg-source: info: applying no_cython_in_binary_package.patch dpkg-source: info: applying any_arch dpkg-source: info: applying no-rpath dpkg-source: info: applying python3.12 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30881/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='ee914f47aab7419fa84f628c5508f108' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='30881' 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.MGHYUDFE/pbuilderrc_rLN8 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MGHYUDFE/b1 --logfile b1/build.log obitools_3.0.1~b26+dfsg-3.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux ff64a 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 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/30881/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-sequence-python3, python3-dev:native, libpython3-dev, python3-setuptools, cython3, cmake dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19689 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-dev:native. pbuilder-satisfydepends-dummy depends on libpython3-dev; however: Package libpython3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake 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} cmake{a} cmake-data{a} cython3{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} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{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} python3.12{a} python3.12-dev{a} python3.12-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 javascript-common krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 47.8 MB of archives. After unpacking 182 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.7-3 [800 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.7-3 [1808 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 12 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1819 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libproc2-0 armhf 2:4.0.4-6 [56.0 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf procps armhf 2:4.0.4-6 [864 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf cmake-data all 3.30.5-1 [2223 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libarchive13t64 armhf 3.7.4-1.1 [306 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libcurl4t64 armhf 8.11.0-1 [303 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libjsoncpp26 armhf 1.9.6-3 [69.9 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf librhash1 armhf 1.4.5-1 [143 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libuv1t64 armhf 1.48.0-7 [134 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf cmake armhf 3.30.5-1 [5365 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf cython3 armhf 3.0.11+dfsg-1+b1 [2812 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 64 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf python3-autocommand all 2.2.2-3 [13.6 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf python3-typeguard all 4.4.1-1 [37.0 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf python3-inflect all 7.3.1-2 [32.4 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf python3-jaraco.context all 6.0.0-1 [7984 B] Get: 76 http://deb.debian.org/debian trixie/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 74.1.2-2 [213 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf python3-zipp all 3.21.0-1 [10.6 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 74.1.2-2 [736 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20241024 [109 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libexpat1-dev armhf 2.6.4-1 [140 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libpython3.12t64 armhf 3.12.7-3 [1848 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libpython3.12-dev armhf 3.12.7-3 [3808 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libpython3-dev armhf 3.12.6-1 [9952 B] Get: 89 http://deb.debian.org/debian trixie/main armhf python3.12-dev armhf 3.12.7-3 [505 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf python3-dev armhf 3.12.6-1 [26.1 kB] Fetched 47.8 MB in 2s (20.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 19689 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.7-3) ... 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 python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_armhf.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:armhf (3.12.7-3) ... Setting up libexpat1:armhf (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20009 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_armhf.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../04-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../06-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../07-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../08-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 .../09-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:armhf. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../14-libreadline8t64_8.2-5_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 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_armhf.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21071 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_armhf.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:armhf. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-6_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-6_armhf.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-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 .../05-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. 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Unpacking libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../26-libnghttp2-14_1.64.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.64.0-1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../27-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 .../28-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 .../29-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl4t64:armhf. Preparing to unpack .../30-libcurl4t64_8.11.0-1_armhf.deb ... Unpacking libcurl4t64:armhf (8.11.0-1) ... Selecting previously unselected package libjsoncpp26:armhf. 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Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../55-python3-pkg-resources_74.1.2-2_all.deb ... Unpacking python3-pkg-resources (74.1.2-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../56-python3-zipp_3.21.0-1_all.deb ... Unpacking python3-zipp (3.21.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../57-python3-setuptools_74.1.2-2_all.deb ... Unpacking python3-setuptools (74.1.2-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../58-dh-python_6.20241024_all.deb ... Unpacking dh-python (6.20241024) ... Selecting previously unselected package libexpat1-dev:armhf. Preparing to unpack .../59-libexpat1-dev_2.6.4-1_armhf.deb ... Unpacking libexpat1-dev:armhf (2.6.4-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../60-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../61-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../62-libjs-sphinxdoc_7.4.7-4_all.deb ... Unpacking libjs-sphinxdoc (7.4.7-4) ... Selecting previously unselected package libpython3.12t64:armhf. Preparing to unpack .../63-libpython3.12t64_3.12.7-3_armhf.deb ... Unpacking libpython3.12t64:armhf (3.12.7-3) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../64-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 libpython3.12-dev:armhf. Preparing to unpack .../65-libpython3.12-dev_3.12.7-3_armhf.deb ... Unpacking libpython3.12-dev:armhf (3.12.7-3) ... Selecting previously unselected package libpython3-dev:armhf. Preparing to unpack .../66-libpython3-dev_3.12.6-1_armhf.deb ... Unpacking libpython3-dev:armhf (3.12.6-1) ... Selecting previously unselected package python3.12-dev. Preparing to unpack .../67-python3.12-dev_3.12.7-3_armhf.deb ... Unpacking python3.12-dev (3.12.7-3) ... Selecting previously unselected package python3-dev. Preparing to unpack .../68-python3-dev_3.12.6-1_armhf.deb ... Unpacking python3-dev (3.12.6-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b6) ... Setting up libuv1t64:armhf (1.48.0-7) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/obitools-3.0.1~b26+dfsg/ && 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 > ../obitools_3.0.1~b26+dfsg-3_source.changes dpkg-buildpackage: info: source package obitools dpkg-buildpackage: info: source version 3.0.1~b26+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. 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compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Configuring done (10.8s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject Compile the shared C library make[1]: Entering directory '/build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject' /usr/bin/cmake -S"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -B"/build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject" --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start 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"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obiblob_indexer.c" [ 9%] Building C object CMakeFiles/cobitools3.dir/obi_lcs.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obi_lcs.c.o -MF CMakeFiles/cobitools3.dir/obi_lcs.c.o.d -o CMakeFiles/cobitools3.dir/obi_lcs.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obi_lcs.c" [ 11%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_str.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_str.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_str.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_str.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_str.c" [ 13%] Building C object CMakeFiles/cobitools3.dir/bloom.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/bloom.c.o -MF CMakeFiles/cobitools3.dir/bloom.c.o.d -o CMakeFiles/cobitools3.dir/bloom.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/bloom.c" [ 15%] Building C object CMakeFiles/cobitools3.dir/build_reference_db.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/build_reference_db.c.o -MF CMakeFiles/cobitools3.dir/build_reference_db.c.o.d -o CMakeFiles/cobitools3.dir/build_reference_db.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/build_reference_db.c" [ 17%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_array.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_array.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_array.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_array.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_array.c" [ 19%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_idx.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_idx.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_idx.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_idx.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_idx.c" [ 21%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_bool.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_bool.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_bool.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_bool.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_bool.c" [ 23%] Building C object CMakeFiles/cobitools3.dir/libjson/json_utils.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libjson/json_utils.c.o -MF CMakeFiles/cobitools3.dir/libjson/json_utils.c.o.d -o CMakeFiles/cobitools3.dir/libjson/json_utils.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libjson/json_utils.c" [ 25%] Building C object CMakeFiles/cobitools3.dir/libjson/cJSON.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libjson/cJSON.c.o -MF CMakeFiles/cobitools3.dir/libjson/cJSON.c.o.d -o CMakeFiles/cobitools3.dir/libjson/cJSON.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libjson/cJSON.c" [ 26%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_blob.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_blob.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_blob.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_blob.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_blob.c" [ 28%] Building C object CMakeFiles/cobitools3.dir/dna_seq_indexer.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/dna_seq_indexer.c.o -MF CMakeFiles/cobitools3.dir/dna_seq_indexer.c.o.d -o CMakeFiles/cobitools3.dir/dna_seq_indexer.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/dna_seq_indexer.c" [ 30%] Building C object CMakeFiles/cobitools3.dir/obi_ecotag.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obi_ecotag.c.o -MF CMakeFiles/cobitools3.dir/obi_ecotag.c.o.d -o CMakeFiles/cobitools3.dir/obi_ecotag.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obi_ecotag.c" [ 32%] Building C object CMakeFiles/cobitools3.dir/encode.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/encode.c.o -MF CMakeFiles/cobitools3.dir/encode.c.o.d -o CMakeFiles/cobitools3.dir/encode.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/encode.c" [ 34%] Building C object CMakeFiles/cobitools3.dir/obiavl.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obiavl.c.o -MF CMakeFiles/cobitools3.dir/obiavl.c.o.d -o CMakeFiles/cobitools3.dir/obiavl.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obiavl.c" [ 36%] Building C object CMakeFiles/cobitools3.dir/sse_banded_LCS_alignment.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/sse_banded_LCS_alignment.c.o -MF CMakeFiles/cobitools3.dir/sse_banded_LCS_alignment.c.o.d -o CMakeFiles/cobitools3.dir/sse_banded_LCS_alignment.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/sse_banded_LCS_alignment.c" [ 38%] Building C object CMakeFiles/cobitools3.dir/kmer_similarity.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/kmer_similarity.c.o -MF CMakeFiles/cobitools3.dir/kmer_similarity.c.o.d -o CMakeFiles/cobitools3.dir/kmer_similarity.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/kmer_similarity.c" [ 40%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_qual.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_qual.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_qual.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_qual.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_qual.c" [ 42%] Building C object CMakeFiles/cobitools3.dir/obi_clean.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obi_clean.c.o -MF CMakeFiles/cobitools3.dir/obi_clean.c.o.d -o CMakeFiles/cobitools3.dir/obi_clean.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obi_clean.c" [ 44%] Building C object CMakeFiles/cobitools3.dir/utils.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/utils.c.o -MF CMakeFiles/cobitools3.dir/utils.c.o.d -o CMakeFiles/cobitools3.dir/utils.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/utils.c" [ 46%] Building C object CMakeFiles/cobitools3.dir/uint8_indexer.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/uint8_indexer.c.o -MF CMakeFiles/cobitools3.dir/uint8_indexer.c.o.d -o CMakeFiles/cobitools3.dir/uint8_indexer.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/uint8_indexer.c" [ 48%] Building C object CMakeFiles/cobitools3.dir/murmurhash2.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/murmurhash2.c.o -MF CMakeFiles/cobitools3.dir/murmurhash2.c.o.d -o CMakeFiles/cobitools3.dir/murmurhash2.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/murmurhash2.c" [ 50%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_char.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_char.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_char.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_char.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_char.c" [ 51%] Building C object CMakeFiles/cobitools3.dir/obiview.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obiview.c.o -MF CMakeFiles/cobitools3.dir/obiview.c.o.d -o CMakeFiles/cobitools3.dir/obiview.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obiview.c" [ 53%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_int.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_int.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_int.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_int.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_int.c" [ 55%] Building C object CMakeFiles/cobitools3.dir/linked_list.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/linked_list.c.o -MF CMakeFiles/cobitools3.dir/linked_list.c.o.d -o CMakeFiles/cobitools3.dir/linked_list.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/linked_list.c" [ 57%] Building C object CMakeFiles/cobitools3.dir/obiblob.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obiblob.c.o -MF CMakeFiles/cobitools3.dir/obiblob.c.o.d -o CMakeFiles/cobitools3.dir/obiblob.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obiblob.c" [ 59%] Building C object CMakeFiles/cobitools3.dir/hashtable.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/hashtable.c.o -MF CMakeFiles/cobitools3.dir/hashtable.c.o.d -o CMakeFiles/cobitools3.dir/hashtable.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/hashtable.c" [ 61%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn.c" [ 63%] Building C object CMakeFiles/cobitools3.dir/char_str_indexer.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/char_str_indexer.c.o -MF CMakeFiles/cobitools3.dir/char_str_indexer.c.o.d -o CMakeFiles/cobitools3.dir/char_str_indexer.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/char_str_indexer.c" [ 65%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_float.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_float.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_float.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_float.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_float.c" [ 67%] Building C object CMakeFiles/cobitools3.dir/upperband.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/upperband.c.o -MF CMakeFiles/cobitools3.dir/upperband.c.o.d -o CMakeFiles/cobitools3.dir/upperband.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/upperband.c" [ 69%] Building C object CMakeFiles/cobitools3.dir/crc64.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/crc64.c.o -MF CMakeFiles/cobitools3.dir/crc64.c.o.d -o CMakeFiles/cobitools3.dir/crc64.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/crc64.c" [ 71%] Building C object CMakeFiles/cobitools3.dir/obidmscolumn_seq.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumn_seq.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumn_seq.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumn_seq.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumn_seq.c" [ 73%] Building C object CMakeFiles/cobitools3.dir/obilittlebigman.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obilittlebigman.c.o -MF CMakeFiles/cobitools3.dir/obilittlebigman.c.o.d -o CMakeFiles/cobitools3.dir/obilittlebigman.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obilittlebigman.c" [ 75%] Building C object CMakeFiles/cobitools3.dir/obidmscolumndir.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidmscolumndir.c.o -MF CMakeFiles/cobitools3.dir/obidmscolumndir.c.o.d -o CMakeFiles/cobitools3.dir/obidmscolumndir.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidmscolumndir.c" [ 76%] Building C object CMakeFiles/cobitools3.dir/obidms.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obidms.c.o -MF CMakeFiles/cobitools3.dir/obidms.c.o.d -o CMakeFiles/cobitools3.dir/obidms.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obidms.c" [ 78%] Building C object CMakeFiles/cobitools3.dir/obi_ecopcr.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obi_ecopcr.c.o -MF CMakeFiles/cobitools3.dir/obi_ecopcr.c.o.d -o CMakeFiles/cobitools3.dir/obi_ecopcr.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obi_ecopcr.c" [ 80%] Building C object CMakeFiles/cobitools3.dir/libecoPCR/libthermo/nnparams.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libecoPCR/libthermo/nnparams.c.o -MF CMakeFiles/cobitools3.dir/libecoPCR/libthermo/nnparams.c.o.d -o CMakeFiles/cobitools3.dir/libecoPCR/libthermo/nnparams.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libecoPCR/libthermo/nnparams.c" [ 82%] Building C object CMakeFiles/cobitools3.dir/libecoPCR/ecoapat.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libecoPCR/ecoapat.c.o -MF CMakeFiles/cobitools3.dir/libecoPCR/ecoapat.c.o.d -o CMakeFiles/cobitools3.dir/libecoPCR/ecoapat.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libecoPCR/ecoapat.c" [ 84%] Building C object CMakeFiles/cobitools3.dir/libecoPCR/libapat/libstki.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libecoPCR/libapat/libstki.c.o -MF CMakeFiles/cobitools3.dir/libecoPCR/libapat/libstki.c.o.d -o CMakeFiles/cobitools3.dir/libecoPCR/libapat/libstki.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libecoPCR/libapat/libstki.c" [ 86%] Building C object CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_search.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_search.c.o -MF CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_search.c.o.d -o CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_search.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libecoPCR/libapat/apat_search.c" [ 88%] Building C object CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_parse.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_parse.c.o -MF CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_parse.c.o.d -o CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_parse.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libecoPCR/libapat/apat_parse.c" [ 90%] Building C object CMakeFiles/cobitools3.dir/libecoPCR/ecodna.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libecoPCR/ecodna.c.o -MF CMakeFiles/cobitools3.dir/libecoPCR/ecodna.c.o.d -o CMakeFiles/cobitools3.dir/libecoPCR/ecodna.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libecoPCR/ecodna.c" [ 92%] Building C object CMakeFiles/cobitools3.dir/libecoPCR/ecoMalloc.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libecoPCR/ecoMalloc.c.o -MF CMakeFiles/cobitools3.dir/libecoPCR/ecoMalloc.c.o.d -o CMakeFiles/cobitools3.dir/libecoPCR/ecoMalloc.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libecoPCR/ecoMalloc.c" [ 94%] Building C object CMakeFiles/cobitools3.dir/libecoPCR/ecoError.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/libecoPCR/ecoError.c.o -MF CMakeFiles/cobitools3.dir/libecoPCR/ecoError.c.o.d -o CMakeFiles/cobitools3.dir/libecoPCR/ecoError.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/libecoPCR/ecoError.c" [ 96%] Building C object CMakeFiles/cobitools3.dir/obitypes.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/obitypes.c.o -MF CMakeFiles/cobitools3.dir/obitypes.c.o.d -o CMakeFiles/cobitools3.dir/obitypes.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/obitypes.c" [ 98%] Building C object CMakeFiles/cobitools3.dir/array_indexer.c.o /usr/bin/cc -Dcobitools3_EXPORTS -I"/build/reproducible-path/obitools-3.0.1~b26+dfsg/src" -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -fPIC -fopenmp -MD -MT CMakeFiles/cobitools3.dir/array_indexer.c.o -MF CMakeFiles/cobitools3.dir/array_indexer.c.o.d -o CMakeFiles/cobitools3.dir/array_indexer.c.o -c "/build/reproducible-path/obitools-3.0.1~b26+dfsg/src/array_indexer.c" [100%] Linking C shared library libcobitools3.so /usr/bin/cmake -E cmake_link_script CMakeFiles/cobitools3.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -O3 -w -I "src" -I "src/libecoPCR" -I "src/libjson" -O3 -DNDEBUG -Wl,-z,relro -shared -Wl,-soname,libcobitools3.so -o libcobitools3.so CMakeFiles/cobitools3.dir/obisig.c.o CMakeFiles/cobitools3.dir/obierrno.c.o CMakeFiles/cobitools3.dir/obidms_taxonomy.c.o CMakeFiles/cobitools3.dir/obiblob_indexer.c.o CMakeFiles/cobitools3.dir/obi_lcs.c.o CMakeFiles/cobitools3.dir/obidmscolumn_str.c.o CMakeFiles/cobitools3.dir/bloom.c.o CMakeFiles/cobitools3.dir/build_reference_db.c.o CMakeFiles/cobitools3.dir/obidmscolumn_array.c.o CMakeFiles/cobitools3.dir/obidmscolumn_idx.c.o CMakeFiles/cobitools3.dir/obidmscolumn_bool.c.o CMakeFiles/cobitools3.dir/libjson/json_utils.c.o CMakeFiles/cobitools3.dir/libjson/cJSON.c.o CMakeFiles/cobitools3.dir/obidmscolumn_blob.c.o CMakeFiles/cobitools3.dir/dna_seq_indexer.c.o CMakeFiles/cobitools3.dir/obi_ecotag.c.o CMakeFiles/cobitools3.dir/encode.c.o CMakeFiles/cobitools3.dir/obiavl.c.o CMakeFiles/cobitools3.dir/sse_banded_LCS_alignment.c.o CMakeFiles/cobitools3.dir/kmer_similarity.c.o CMakeFiles/cobitools3.dir/obidmscolumn_qual.c.o CMakeFiles/cobitools3.dir/obi_clean.c.o CMakeFiles/cobitools3.dir/utils.c.o CMakeFiles/cobitools3.dir/uint8_indexer.c.o CMakeFiles/cobitools3.dir/murmurhash2.c.o CMakeFiles/cobitools3.dir/obidmscolumn_char.c.o CMakeFiles/cobitools3.dir/obiview.c.o CMakeFiles/cobitools3.dir/obidmscolumn_int.c.o CMakeFiles/cobitools3.dir/linked_list.c.o CMakeFiles/cobitools3.dir/obiblob.c.o CMakeFiles/cobitools3.dir/hashtable.c.o CMakeFiles/cobitools3.dir/obidmscolumn.c.o CMakeFiles/cobitools3.dir/char_str_indexer.c.o CMakeFiles/cobitools3.dir/obidmscolumn_float.c.o CMakeFiles/cobitools3.dir/upperband.c.o CMakeFiles/cobitools3.dir/crc64.c.o CMakeFiles/cobitools3.dir/obidmscolumn_seq.c.o CMakeFiles/cobitools3.dir/obilittlebigman.c.o CMakeFiles/cobitools3.dir/obidmscolumndir.c.o CMakeFiles/cobitools3.dir/obidms.c.o CMakeFiles/cobitools3.dir/obi_ecopcr.c.o CMakeFiles/cobitools3.dir/libecoPCR/libthermo/nnparams.c.o CMakeFiles/cobitools3.dir/libecoPCR/ecoapat.c.o CMakeFiles/cobitools3.dir/libecoPCR/libapat/libstki.c.o CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_search.c.o CMakeFiles/cobitools3.dir/libecoPCR/libapat/apat_parse.c.o CMakeFiles/cobitools3.dir/libecoPCR/ecodna.c.o CMakeFiles/cobitools3.dir/libecoPCR/ecoMalloc.c.o CMakeFiles/cobitools3.dir/libecoPCR/ecoError.c.o CMakeFiles/cobitools3.dir/obitypes.c.o CMakeFiles/cobitools3.dir/array_indexer.c.o /usr/lib/gcc/arm-linux-gnueabihf/14/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.a make[3]: Leaving directory '/build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject' [100%] Built target cobitools3 make[2]: Leaving directory '/build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject' /usr/bin/cmake -E cmake_progress_start "/build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject/CMakeFiles" 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/obitools-3.0.1~b26+dfsg/libcobitools3.so make[1]: Leaving directory '/build/reproducible-path/obitools-3.0.1~b26+dfsg/build/cobject' running build_py creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3 copying python/obitools3/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3 copying python/obitools3/version.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3 creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign copying python/obitools3/libalign/solexapairend.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign copying python/obitools3/libalign/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/writers copying python/obitools3/writers/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/writers creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/uri copying python/obitools3/uri/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/uri creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/apps copying python/obitools3/apps/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/apps creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/apps/optiongroups copying python/obitools3/apps/optiongroups/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/apps/optiongroups creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/parsers copying python/obitools3/parsers/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/parsers creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms copying python/obitools3/dms/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/taxo copying python/obitools3/dms/taxo/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/taxo creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/view copying python/obitools3/dms/view/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/view creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/view/typed_view copying python/obitools3/dms/view/typed_view/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/view/typed_view creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/column copying python/obitools3/dms/column/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/column creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/column/typed_column copying python/obitools3/dms/column/typed_column/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/column/typed_column creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/capi copying python/obitools3/dms/capi/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/dms/capi creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/format copying python/obitools3/format/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/format creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/files copying python/obitools3/files/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/files creating /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/commands copying python/obitools3/commands/__init__.py -> /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/commands running build_ext building 'obitools3.utils' extension creating build/temp.linux-armv7l-cpython-312 creating build/temp.linux-armv7l-cpython-312/build creating build/temp.linux-armv7l-cpython-312/build/python creating build/temp.linux-armv7l-cpython-312/build/python/obitools3 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/utils.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/utils.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/utils.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/utils.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._dynamic' extension creating build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_dynamic.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_dynamic.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_dynamic.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_dynamic.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._nws' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_nws.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_nws.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_nws.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_nws.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._rassemble' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_rassemble.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_rassemble.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_rassemble.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_rassemble.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign.apat_pattern' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/apat_pattern.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/apat_pattern.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/apat_pattern.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/apat_pattern.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._qsrassemble' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_qsrassemble.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_qsrassemble.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_qsrassemble.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_qsrassemble.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._freeendgapfm' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_freeendgapfm.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_freeendgapfm.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_freeendgapfm.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_freeendgapfm.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._qsassemble' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_qsassemble.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_qsassemble.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_qsassemble.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_qsassemble.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._freeendgap' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_freeendgap.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_freeendgap.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_freeendgap.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_freeendgap.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign.shifted_ali' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/shifted_ali.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/shifted_ali.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/shifted_ali.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/shifted_ali.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._assemble' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_assemble.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_assemble.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_assemble.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_assemble.cpython-312-arm-linux-gnueabihf.so building 'obitools3.libalign._solexapairend' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/libalign/_solexapairend.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_solexapairend.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/libalign/_solexapairend.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/libalign/_solexapairend.cpython-312-arm-linux-gnueabihf.so building 'obitools3.writers.fastq' extension creating build/temp.linux-armv7l-cpython-312/build/python/obitools3/writers arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/writers/fastq.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/writers/fastq.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/writers/fastq.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/writers/fastq.cpython-312-arm-linux-gnueabihf.so building 'obitools3.writers.fasta' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/writers/fasta.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/writers/fasta.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/writers/fasta.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/writers/fasta.cpython-312-arm-linux-gnueabihf.so building 'obitools3.writers.tab' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/writers/tab.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/writers/tab.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/writers/tab.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/writers/tab.cpython-312-arm-linux-gnueabihf.so building 'obitools3.uri.decode' extension creating build/temp.linux-armv7l-cpython-312/build/python/obitools3/uri arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/uri/decode.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/uri/decode.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/uri/decode.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/uri/decode.cpython-312-arm-linux-gnueabihf.so building 'obitools3.apps.config' extension creating build/temp.linux-armv7l-cpython-312/build/python/obitools3/apps arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/apps/config.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/apps/config.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/apps/config.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/apps/config.cpython-312-arm-linux-gnueabihf.so building 'obitools3.apps.arguments' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/apps/arguments.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/apps/arguments.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/apps/arguments.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/apps/arguments.cpython-312-arm-linux-gnueabihf.so building 'obitools3.apps.logging' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/apps/logging.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/apps/logging.o -w -fPIC arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/build/python/obitools3/apps/logging.o -L/usr/lib/python3/dist-packages -L/build/reproducible-path/obitools-3.0.1~b26+dfsg -L/usr/lib/arm-linux-gnueabihf -lcobitools3 -o /build/reproducible-path/obitools-3.0.1~b26+dfsg/.pybuild/cpython3_3.12_obitools3/build/obitools3/apps/logging.cpython-312-arm-linux-gnueabihf.so building 'obitools3.apps.progress' extension arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -O3 -w -I src -I src/libecoPCR -I src/libjson -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -Isrc/libecoPCR -Isrc/libjson -I/usr/include/python3.12 -c build/python/obitools3/apps/progress.c -o build/temp.linux-armv7l-cpython-312/build/python/obitools3/apps/progress.o -w -fPIC build/python/obitools3/apps/progress.c: In function '__pyx_pf_9obitools3_4apps_8progress_11ProgressBar_2__call__': build/python/obitools3/apps/progress.c:3882:22: error: passing argument 1 of 'gmtime_r' from incompatible pointer type [-Wincompatible-pointer-types] 3882 | ((void)gmtime_r((&__pyx_v_more), (&__pyx_v_remain))); | ~^~~~~~~~~~~~~~ | | | clock_t * {aka long int *} In file included from /usr/include/features.h:510, from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, from /usr/include/stdlib.h:26, from /usr/include/python3.12/Python.h:23, from build/python/obitools3/apps/progress.c:48: /usr/include/time.h:163:18: note: expected 'const time_t * restrict' {aka 'const long long int * restrict'} but argument is of type 'clock_t *' {aka 'long int *'} 163 | extern struct tm*__REDIRECT_NTH (gmtime_r, (const time_t *__restrict __timer, | ^~~~~~~~~~~~~~ error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build dh_auto_build: error: pybuild --build -i python{version} -p 3.12 returned exit code 13 make: *** [debian/rules:15: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/30881 and its subdirectories Thu Nov 28 05:36:28 UTC 2024 W: No second build log, what happened?