Sun Apr 28 08:32:16 UTC 2024 I: starting to build seer/trixie/arm64 on jenkins on '2024-04-28 08:31' Sun Apr 28 08:32:16 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/16155/console.log Sun Apr 28 08:32:16 UTC 2024 I: Downloading source for trixie/seer=1.1.4-7 --2024-04-28 08:32:17-- http://deb.debian.org/debian/pool/main/s/seer/seer_1.1.4-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2172 (2.1K) [text/prs.lines.tag] Saving to: ‘seer_1.1.4-7.dsc’ 0K .. 100% 275M=0s 2024-04-28 08:32:17 (275 MB/s) - ‘seer_1.1.4-7.dsc’ saved [2172/2172] Sun Apr 28 08:32:17 UTC 2024 I: seer_1.1.4-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: seer Binary: seer Architecture: any Version: 1.1.4-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/johnlees/seer Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/seer Vcs-Git: https://salsa.debian.org/med-team/seer.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libarmadillo-dev, libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-dev Package-List: seer deb science optional arch=any Checksums-Sha1: 01aa93df82b6e563f5e06ae47592ae0d98dce2da 972155 seer_1.1.4.orig.tar.gz 3c37d5d36b4a70310ee2006045bafee49086e129 9180 seer_1.1.4-7.debian.tar.xz Checksums-Sha256: 96e55b9fe2cde089ff05bbcd55088832e90f44a968a81a8dca9f9cffa6faa9c1 972155 seer_1.1.4.orig.tar.gz e5ce6e926a188bdba50a2c3665be704ac5c017a4bc1404cac442d8c553014e51 9180 seer_1.1.4-7.debian.tar.xz Files: e4b331eaf17819aabc545b032148d8c2 972155 seer_1.1.4.orig.tar.gz 89a12c9aed3712fc7d5815c0d9eae452 9180 seer_1.1.4-7.debian.tar.xz Dgit: f316ebd0f54934e69591f8ef62849d3d3a6f2da1 debian archive/debian/1.1.4-7 https://git.dgit.debian.org/seer -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmNnx+YUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqe2BAAnXHo/Gm/vEFMS80O/nHEVPcISV9q t9O0NPi6iZPu5XmZYyXM/k0Lrlu2/5m4R2wi8X0GXBWuD9dXRK/kzAsn6F4/p+L7 xRCUAQ6Kt+SjgqF04dyHgR3KraI7JV24vaipyvt6Gz4/+hSRpKpIKWJxzxvAvpdW u3W725twcOn61lgtY5QNzMF0pUoHt9irkp24Q/upU3Tjd+sYOlCeDMLgWGhaOOyj LXg95oLsWe7Ja/YxYvaWrk/H5AT2f89Seajs/PMIFM+oki55gh1VxYH47Kphw/n6 xLAo5R+f1222gDP5uUcyaM/G/+QeCwGa6zceVy6TU+qK/6AM5IGsRNl9UvCwUHX4 bXcXh6hOoRV2xxRPrVpW1XEM5PmqgaMkRUgrFxTxhQi3UBrR8inAm/m5Ti6IbVdT MWKWuNsS1PAghueRPe6iU0NUzhQMhrXOfvN/i7GrvqPnLXOf2jMsVMVqovBMz1Bv DEPt91k5raeWlWeFP00DkPgtvz6XLfhkq0nqFo0jVuGUlRzKqWn+awk7lKRudOkk p5i4WBX9fUdOfa2MwAowrzK2Pq2vHOX/8Frv9yr5c8W3nT+A8AIgvuXNiY/wUfxV 8/JlbDoUnHW+fn0zVKFhwKHneP30ShhDrQuBoLaq95D63Th3oHa1MISfeSNnOYkw JLvKS6OIiLadpoc= =fx4x -----END PGP SIGNATURE----- Sun Apr 28 08:32:17 UTC 2024 I: Checking whether the package is not for us Sun Apr 28 08:32:17 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Sun Apr 28 08:32:17 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Sun Apr 28 08:35:03 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 27 20:32:20 -12 2024 I: pbuilder-time-stamp: 1714293140 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 [seer_1.1.4-7.dsc] I: copying [./seer_1.1.4.orig.tar.gz] I: copying [./seer_1.1.4-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Nov 6 14:42:46 2022 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./seer_1.1.4-7.dsc: no acceptable signature found dpkg-source: info: extracting seer in seer-1.1.4 dpkg-source: info: unpacking seer_1.1.4.orig.tar.gz dpkg-source: info: unpacking seer_1.1.4-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_lib_location.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying gcc11.patch dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/262229/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='1e2c5595993b49d4af0ed933c7edb89c' 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='262229' 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.S3mCo3hb/pbuilderrc_IisD --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.S3mCo3hb/b1 --logfile b1/build.log seer_1.1.4-7.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:15 /bin -> usr/bin I: user script /srv/workspace/pbuilder/262229/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libarmadillo-dev, libdlib-dev, libhdf5-dev, libgzstream-dev, libboost-dev, libboost-program-options-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 ... 19940 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 libarmadillo-dev; however: Package libarmadillo-dev is not installed. pbuilder-satisfydepends-dummy depends on libdlib-dev; however: Package libdlib-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libgzstream-dev; however: Package libgzstream-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-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-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libbsd0{a} libdebhelper-perl{a} libdlib-data{a} libdlib-dev{a} libdlib19.1t64{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgzstream-dev{a} libgzstream0{a} libhwloc15{a} libicu72{a} libjpeg62-turbo{a} liblapack3{a} libllvm17{a} libmagic-mgc{a} libmagic1{a} libopencv-core-dev{a} libopencv-core406{a} libpipeline1{a} libpng-dev{a} libpng16-16t64{a} libpthread-stubs0-dev{a} libpython3-dev{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsensors-config{a} libsensors5{a} libsqlite3-dev{a} libsub-override-perl{a} libtbb-dev{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtool{a} libuchardet0{a} libvulkan1{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxml2{a} libxshmfence1{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} pybind11-dev{a} readline-common{a} sensible-utils{a} tzdata{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libeigen3-dev libhwloc-plugins libltdl-dev libmail-sendmail-perl libpng-tools lynx mesa-vulkan-drivers wget 0 packages upgraded, 111 newly installed, 0 to remove and 0 not upgraded. Need to get 157 MB of archives. After unpacking 639 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libarmadillo-dev but it is not installable Depends: libhdf5-dev but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libssl3 [3.1.5-1 (now)] Install the following packages: 2) hdf5-helpers [1.10.10+repack-3+b1 (testing)] 3) libaec-dev [1.1.3-1 (testing)] 4) libaec0 [1.1.3-1 (testing)] 5) libarmadillo-dev [1:12.6.7+dfsg-1 (testing)] 6) libarmadillo12 [1:12.6.7+dfsg-1 (testing)] 7) libarpack2 [3.9.1-1+b1 (testing)] 8) libarpack2-dev [3.9.1-1+b1 (testing)] 9) libblis-serial-dev [0.9.0-1+b2 (testing)] 10) libblis4-serial [0.9.0-1+b2 (testing)] 11) libbrotli1 [1.1.0-2+b3 (testing)] 12) libcurl3t64-gnutls [8.7.1-3 (testing)] 13) libcurl4-gnutls-dev [8.7.1-3 (testing)] 14) libcurl4t64 [8.7.1-3 (testing)] 15) libhdf5-103-1 [1.10.10+repack-3+b1 (testing)] 16) libhdf5-cpp-103-1 [1.10.10+repack-3+b1 (testing)] 17) libhdf5-dev [1.10.10+repack-3+b1 (testing)] 18) libhdf5-fortran-102 [1.10.10+repack-3+b1 (testing)] 19) libhdf5-hl-100 [1.10.10+repack-3+b1 (testing)] 20) libhdf5-hl-cpp-100 [1.10.10+repack-3+b1 (testing)] 21) libhdf5-hl-fortran-100 [1.10.10+repack-3+b1 (testing)] 22) libjpeg62-turbo-dev [1:2.1.5-2+b2 (testing)] 23) liblapack-dev [3.12.0-3 (testing)] 24) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 25) libnghttp2-14 [1.59.0-1 (testing)] 26) libpsl5t64 [0.21.2-1.1 (testing)] 27) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 28) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 29) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 30) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 31) libssl-dev [3.2.1-3 (testing)] 32) libssl3t64 [3.2.1-3 (testing)] 33) libsuperlu-dev [6.0.1+dfsg1-1+b1 (testing)] 34) libsuperlu6 [6.0.1+dfsg1-1+b1 (testing)] 35) libsz2 [1.1.3-1 (testing)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{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} libarmadillo-dev{a} libarmadillo12{a} libarpack2{a} libarpack2-dev{a} libblas3{a} libblis-serial-dev{a} libblis4-serial{a} libboost-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libbsd0{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdlib-data{a} libdlib-dev{a} libdlib19.1t64{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgzstream-dev{a} libgzstream0{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhwloc15{a} libicu72{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm17{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopencv-core-dev{a} libopencv-core406{a} libpipeline1{a} libpng-dev{a} libpng16-16t64{a} libpsl5t64{a} libpthread-stubs0-dev{a} libpython3-dev{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libssl3t64{a} libsub-override-perl{a} libsuperlu-dev{a} libsuperlu6{a} libsz2{a} libtbb-dev{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtool{a} libuchardet0{a} libvulkan1{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxml2{a} libxshmfence1{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} pybind11-dev{a} readline-common{a} sensible-utils{a} tzdata{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages will be REMOVED: libssl3{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libeigen3-dev libhwloc-plugins libldap-common libltdl-dev libmail-sendmail-perl libpng-tools libsasl2-modules lynx mesa-vulkan-drivers publicsuffix wget 0 packages upgraded, 145 newly installed, 1 to remove and 0 not upgraded. Need to get 175 MB of archives. After unpacking 726 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 28 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 hdf5-helpers arm64 1.10.10+repack-3+b1 [23.5 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1 [22.1 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1 [7664 B] Get: 39 http://deb.debian.org/debian trixie/main arm64 libaec-dev arm64 1.1.3-1 [19.7 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libblis4-serial arm64 0.9.0-1+b2 [791 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libarpack2 arm64 3.9.1-1+b1 [81.2 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libsuperlu6 arm64 6.0.1+dfsg1-1+b1 [141 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libarmadillo12 arm64 1:12.6.7+dfsg-1 [102 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libblis-serial-dev arm64 0.9.0-1+b2 [884 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.0-3 [3584 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libarpack2-dev arm64 3.9.1-1+b1 [98.2 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.7.1-3 [412 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libhdf5-103-1 arm64 1.10.10+repack-3+b1 [1036 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libhdf5-fortran-102 arm64 1.10.10+repack-3+b1 [87.9 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-100 arm64 1.10.10+repack-3+b1 [59.9 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-fortran-100 arm64 1.10.10+repack-3+b1 [38.5 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libhdf5-cpp-103-1 arm64 1.10.10+repack-3+b1 [119 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-cpp-100 arm64 1.10.10+repack-3+b1 [21.1 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-2+b2 [172 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-2+b2 [293 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-3 [523 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.2.1-3 [3089 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libhdf5-dev arm64 1.10.10+repack-3+b1 [2691 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libsuperlu-dev arm64 6.0.1+dfsg1-1+b1 [21.8 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libarmadillo-dev arm64 1:12.6.7+dfsg-1 [408 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-2+b2 [10.6 MB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 76 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83.0 arm64 1.83.0-2+b2 [332 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83-dev arm64 1.83.0-2+b2 [369 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 79 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libdlib-data all 19.24+dfsg-1.1 [63.4 MB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libdlib19.1t64 arm64 19.24+dfsg-1.1 [3688 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libglvnd0 arm64 1.7.0-1+b1 [41.7 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.120-2 [7688 B] Get: 90 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.120-2 [37.5 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libglapi-mesa arm64 23.3.5-1 [45.5 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libx11-xcb1 arm64 2:1.8.7-1+b1 [232 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libxcb-present0 arm64 1.15-1 [106 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libxfixes3 arm64 1:6.0.0-2+b1 [20.5 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libxshmfence1 arm64 1.3-1+b1 [9080 B] Get: 105 http://deb.debian.org/debian trixie/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libvulkan1 arm64 1.3.280.0-1 [119 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.120-2 [21.0 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libdrm-nouveau2 arm64 2.4.120-2 [18.7 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libdrm-radeon1 arm64 2.4.120-2 [21.1 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libllvm17 arm64 1:17.0.6-5 [21.3 MB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libsensors5 arm64 1:3.6.0-9 [33.9 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libgl1-mesa-dri arm64 23.3.5-1 [6928 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libglx-mesa0 arm64 23.3.5-1 [150 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libglx0 arm64 1.7.0-1+b1 [31.0 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libtbbmalloc2 arm64 2021.11.0-2 [35.0 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.10.0-1+b1 [140 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libtbbbind-2-5 arm64 2021.11.0-2 [13.7 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libtbb12 arm64 2021.11.0-2 [63.1 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libopencv-core406 arm64 4.6.0+dfsg-13+b3 [875 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libtbb-dev arm64 2021.11.0-2 [193 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libopencv-core-dev arm64 4.6.0+dfsg-13+b3 [1627 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libpng-dev arm64 1.6.43-5 [356 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libsqlite3-dev arm64 3.45.1-1 [1040 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 x11proto-dev all 2024.1-1 [603 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libxau-dev arm64 1:1.0.9-1+b1 [21.5 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libxdmcp-dev arm64 1:1.1.2-3+b1 [40.6 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libpthread-stubs0-dev arm64 0.4-1+b1 [5324 B] Get: 133 http://deb.debian.org/debian trixie/main arm64 libxcb1-dev arm64 1.15-1 [182 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libx11-dev arm64 2:1.8.7-1+b1 [861 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.8-1 [811 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1781 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libpython3.11 arm64 3.11.8-1 [1844 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.2-1 [278 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libpython3.11-dev arm64 3.11.8-1 [4289 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.11.6-1 [9460 B] Get: 142 http://deb.debian.org/debian trixie/main arm64 pybind11-dev all 2.11.1-2 [191 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libdlib-dev arm64 19.24+dfsg-1.1 [2024 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libgzstream0 arm64 1.5+git20171107.9a20658-2 [7288 B] Get: 145 http://deb.debian.org/debian trixie/main arm64 libgzstream-dev arm64 1.5+git20171107.9a20658-2 [7488 B] Fetched 175 MB in 3s (55.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19940 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19927 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... Selecting previously unselected package tzdata. (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 ... 19942 files and directories currently installed.) Preparing to unpack .../000-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package readline-common. Preparing to unpack .../002-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../005-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../011-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package media-types. Preparing to unpack .../013-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/seer-1.1.4/ && 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 > ../seer_1.1.4-7_source.changes dpkg-buildpackage: info: source package seer dpkg-buildpackage: info: source version 1.1.4-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' cd src && make clean make[2]: Entering directory '/build/reproducible-path/seer-1.1.4/src' rm -f *.o ~* seer kmds map_back combineKmers filter_seer make[2]: Leaving directory '/build/reproducible-path/seer-1.1.4/src' cd test && make clean make[2]: Entering directory '/build/reproducible-path/seer-1.1.4/test' rm -f *.o ~* tests_passed make[2]: Leaving directory '/build/reproducible-path/seer-1.1.4/test' make[1]: Leaving directory '/build/reproducible-path/seer-1.1.4' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' dh_auto_build -- LDFLAGS+=-L/usr/lib/aarch64-linux-gnu/hdf5/serial make -j12 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/aarch64-linux-gnu/hdf5/serial make[2]: Entering directory '/build/reproducible-path/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/reproducible-path/seer-1.1.4/src' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o sample.o sample.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o significant_kmer.o significant_kmer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmer.o kmer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o covar.o covar.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCommon.o seerCommon.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerErr.o seerErr.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerIO.o seerIO.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBasicFilter.o seerBasicFilter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerMain.o seerMain.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCmdLine.o seerCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerStats.o seerStats.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerContinuousAssoc.o seerContinuousAssoc.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, from seer.hpp:10, from seerContinuousAssoc.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/armadillo:26, from kmer.hpp:9, from kmer.cpp:8: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, from seer.hpp:10, from seerStats.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerBinaryAssoc.o seerBinaryAssoc.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from seerCommon.cpp:9: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from seerErr.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, from seer.hpp:10, from seerMain.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, from seer.hpp:10, from seerCmdLine.cpp:9: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from seerBasicFilter.cpp:10: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from seerIO.cpp:12: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, from seer.hpp:10, from seerBinaryAssoc.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o logitFunction.o logitFunction.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, from logitFunction.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o linearFunction.o linearFunction.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from linkFunction.hpp:6, from linearFunction.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsMain.o kmdsMain.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from kmds.hpp:9, from kmdsMain.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsStruct.o kmdsStruct.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from kmds.hpp:9, from kmdsStruct.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmdsCmdLine.o kmdsCmdLine.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from seercommon.hpp:30, from kmds.hpp:9, from kmdsCmdLine.cpp:8: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o fasta.o fasta.cpp In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapMain.o mapMain.cpp In file included from /usr/include/armadillo:26, from seercommon.hpp:35: /usr/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /usr/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /usr/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details' 329 | #pragma message ("INFO: see the documentation for details") | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o mapCmdLine.o mapCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineInit.o combineInit.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineCmdLine.o combineCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o combineKmers.o combineKmers.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filter_seer.o filter_seer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o filterCmdLine.o filterCmdLine.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial combineInit.o combineCmdLine.o combineKmers.o -lgzstream -lz -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial -o combineKmers g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial significant_kmer.o filter_seer.o filterCmdLine.o -lboost_program_options -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial -o filter_seer g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial fasta.o significant_kmer.o mapMain.o mapCmdLine.o -lboost_program_options -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial -o map_back g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o seerMain.o seerCmdLine.o seerStats.o seerContinuousAssoc.o seerBinaryAssoc.o logitFunction.o linearFunction.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial -o seer g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/seer-1.1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial sample.o significant_kmer.o kmer.o covar.o seerCommon.o seerErr.o seerIO.o seerBasicFilter.o kmdsMain.o kmdsStruct.o kmdsCmdLine.o -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -lpthread -Wl,-z,relro -Wl,-z,now -L/usr/lib/aarch64-linux-gnu/hdf5/serial -o kmds make[3]: Leaving directory '/build/reproducible-path/seer-1.1.4/src' make[2]: Leaving directory '/build/reproducible-path/seer-1.1.4' make[1]: Leaving directory '/build/reproducible-path/seer-1.1.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' if dh_auto_test ; then echo Test passed ; else echo '****************************** TEST FAILED. Please contact upstream *******************************' ; fi make -j12 test make[2]: Entering directory '/build/reproducible-path/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/reproducible-path/seer-1.1.4/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/seer-1.1.4/src' cd test && make test make[3]: Entering directory '/build/reproducible-path/seer-1.1.4/test' ./run_test.pl && touch tests_passed PASSED test 1, basic filters PASSED test 2, binary phenotype assocation PASSED test 3, print output PASSED test 4, continuous phenotype assocation PASSED test 5, assocation with population structure PASSED test 6, assocation with covariates PASSED test 7, filter output PASSED test 8, map k-mers make[3]: Leaving directory '/build/reproducible-path/seer-1.1.4/test' make[2]: Leaving directory '/build/reproducible-path/seer-1.1.4' Test passed make[1]: Leaving directory '/build/reproducible-path/seer-1.1.4' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' dh_auto_install -- PREFIX=/build/reproducible-path/seer-1.1.4/debian/seer/usr make -j12 install DESTDIR=/build/reproducible-path/seer-1.1.4/debian/seer AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/seer-1.1.4/debian/seer/usr make[2]: Entering directory '/build/reproducible-path/seer-1.1.4' cd src && make all make[3]: Entering directory '/build/reproducible-path/seer-1.1.4/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/seer-1.1.4/src' cd src && make install make[3]: Entering directory '/build/reproducible-path/seer-1.1.4/src' install -d /build/reproducible-path/seer-1.1.4/debian/seer/usr/bin install seer kmds map_back combineKmers filter_seer /build/reproducible-path/seer-1.1.4/debian/seer/usr/bin make[3]: Leaving directory '/build/reproducible-path/seer-1.1.4/src' make[2]: Leaving directory '/build/reproducible-path/seer-1.1.4' for pl in scripts/*.pl ; do \ plbase=`basename ${pl} .pl` ; \ sed "s+Usage: ./${plbase}.pl+Usage: ${plbase}+" ${pl} > /build/reproducible-path/seer-1.1.4/debian/seer/usr/bin/${plbase} ; \ done # Fix broken usage hint: sed -i "s+Usage: ./hits_to_matrix.pl+Usage: reformat_output+" /build/reproducible-path/seer-1.1.4/debian/seer/usr/bin/reformat_output make[1]: Leaving directory '/build/reproducible-path/seer-1.1.4' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/seer-1.1.4' dh_fixperms find debian -name Makefile -exec chmod -x \{\} \; find debian -name "*.fa" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/seer-1.1.4' 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/seer/usr/bin/combineKmers was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'seer' in '../seer_1.1.4-7_arm64.deb'. dpkg-deb: building package 'seer-dbgsym' in '../seer-dbgsym_1.1.4-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../seer_1.1.4-7_arm64.buildinfo dpkg-genchanges --build=binary -O../seer_1.1.4-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original 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/262229 and its subdirectories I: Current time: Sat Apr 27 20:35:01 -12 2024 I: pbuilder-time-stamp: 1714293301 Sun Apr 28 08:35:03 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sun Apr 28 08:35:03 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sun Apr 28 08:36:43 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sun Apr 28 08:36:43 UTC 2024 I: seer_1.1.4-7_arm64.changes: Format: 1.8 Date: Sun, 06 Nov 2022 15:38:02 +0100 Source: seer Binary: seer seer-dbgsym Architecture: arm64 Version: 1.1.4-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: seer - genomic sequence element (kmer) enrichment analysis Changes: seer (1.1.4-7) unstable; urgency=medium . * d/watch: repair github changes; move to git mode. * Standards-Version: 4.6.1 (routine-update) * typos.patch: add; fix typos caught by lintian. * d/m/blastn_to_phandango.1: new manual page. * d/control: add myself to uploaders. * d/copyright: refresh debian/ copyright years. Checksums-Sha1: bd90216d053fd18b2f4031925eba58587a62e078 8564028 seer-dbgsym_1.1.4-7_arm64.deb 2da4faccd159bd7ea245c3a24c67841fb0c30da7 9237 seer_1.1.4-7_arm64.buildinfo dd09636823c795332b9faf42f2e41c472fef3b6e 1141532 seer_1.1.4-7_arm64.deb Checksums-Sha256: 4d4901808dee961b6c2dd84242b450ff0242b7d13822ca3baea4dac22b06adc7 8564028 seer-dbgsym_1.1.4-7_arm64.deb 9bcfd123ff2011731ada685dbb8b73b4fceba1758cad2b9f97846f3cc763dcd7 9237 seer_1.1.4-7_arm64.buildinfo 2e03067e67115343b88994cb58bb52d4e53a53da50ef59752f79804f67a29a51 1141532 seer_1.1.4-7_arm64.deb Files: 4fd36877a378baba95b666c7253f3b80 8564028 debug optional seer-dbgsym_1.1.4-7_arm64.deb b44f2c82a54a181d1f4fc1b56de371ee 9237 science optional seer_1.1.4-7_arm64.buildinfo 466500a7e8b84b47ba1d9f924d901d3c 1141532 science optional seer_1.1.4-7_arm64.deb Sun Apr 28 08:36:45 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_20-16155.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.S3mCo3hb/seer_1.1.4-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.S3mCo3hb/seer_1.1.4-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.S3mCo3hb/seer_1.1.4-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.S3mCo3hb/b1/seer_1.1.4-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.S3mCo3hb/b2/seer_1.1.4-7_arm64.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: 0.927s) 0.927s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.136s) 0.136s 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: 1.401s CPU time consumed: 1.340s Sun Apr 28 08:36:47 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 28 08:36:47 UTC 2024 I: seer from trixie built successfully and reproducibly on arm64. Sun Apr 28 08:36:48 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Apr 28 08:36:48 UTC 2024 I: Submitting 12K b1/seer_1.1.4-7_arm64.buildinfo.asc Sun Apr 28 08:36:49 UTC 2024 I: Submitting 12K b2/seer_1.1.4-7_arm64.buildinfo.asc Sun Apr 28 08:36:50 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 28 08:36:50 UTC 2024 I: Done submitting .buildinfo files. Sun Apr 28 08:36:50 UTC 2024 I: Removing signed seer_1.1.4-7_arm64.buildinfo.asc files: removed './b1/seer_1.1.4-7_arm64.buildinfo.asc' removed './b2/seer_1.1.4-7_arm64.buildinfo.asc'