Mon Jan 27 16:10:22 UTC 2025 I: starting to build libbpp-phyl-omics/unstable/armhf on jenkins on '2025-01-27 16:10' Mon Jan 27 16:10:22 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_10/6991/console.log Mon Jan 27 16:10:22 UTC 2025 I: Downloading source for unstable/libbpp-phyl-omics=2.4.1-7 --2025-01-27 16:10:22-- http://deb.debian.org/debian/pool/main/libb/libbpp-phyl-omics/libbpp-phyl-omics_2.4.1-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2273 (2.2K) [text/prs.lines.tag] Saving to: ‘libbpp-phyl-omics_2.4.1-7.dsc’ 0K .. 100% 400M=0s 2025-01-27 16:10:22 (400 MB/s) - ‘libbpp-phyl-omics_2.4.1-7.dsc’ saved [2273/2273] Mon Jan 27 16:10:22 UTC 2025 I: libbpp-phyl-omics_2.4.1-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libbpp-phyl-omics Binary: libbpp-phyl-omics-dev, libbpp-phyl-omics3t64 Architecture: any Version: 2.4.1-7 Maintainer: Debian Med Packaging Team Uploaders: Julien Dutheil , Andreas Tille Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/libbpp-phyl-omics Vcs-Git: https://salsa.debian.org/med-team/libbpp-phyl-omics.git Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), cmake, d-shlibs (>= 0.106~), libbpp-phyl-dev, libbpp-seq-omics-dev Package-List: libbpp-phyl-omics-dev deb libdevel optional arch=any libbpp-phyl-omics3t64 deb libs optional arch=any Checksums-Sha1: b3132c35963eec7890514c1766b6c13f5c661a31 48482 libbpp-phyl-omics_2.4.1.orig.tar.gz f07d9e671ce92f33785fb09e6e422cb040048cb4 10632 libbpp-phyl-omics_2.4.1-7.debian.tar.xz Checksums-Sha256: fb0908422e59c71065db874e68d5c71acddf66d8a51776f7e04a5f8d5f0f6577 48482 libbpp-phyl-omics_2.4.1.orig.tar.gz 4d614b594eaf300295bc8917f4ef099983f308d8cf0cd94e1c7c5bf80e9cafcd 10632 libbpp-phyl-omics_2.4.1-7.debian.tar.xz Files: 7c1c1d06e0c0ff61ddecc7fcc4064f51 48482 libbpp-phyl-omics_2.4.1.orig.tar.gz 729df38076498102b04f2079f46081db 10632 libbpp-phyl-omics_2.4.1-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmaIG78RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEU0w/+L4emwpTj/eFImhXcCnJe0o/7cILtBJos EVyqrHF68gE0/AA65XyiSoN0jL3yFaHFWpYrjRXyODdqHtibA5FVM3N/dXziKIE2 AmHfJLKGRrysJWxoCRvS8hEI2P6NeuUonM+iJUDcy7oT8sdZgDi8HJd/W4iBUWnF YshHsHgt6oFamW6O5texvoKAZL8s71WRQw2PUXL7Rd/Rf76s+F0iqlJ9WY+wnHpP Mk+Vi6WsG1NYsNHRVUIJe+zn7DBxl4Xx0IYrIHl7OHet7SmdawkHc6V3TMcoATkA 3coeJ/CS5jTzW0elsCwcRBrdup7oow43LhGImoblIjQbjRpZ+DnqbJLJoath1AWr fkiNk48zLU0HntrDruuxNUPgja62z6VnLh+T404QFTmNgKMq8e50czDzWQhUjFfi yzOv6HH3XvliGZJ4l+ZnKv5PzKErHzzN1ARqtM12suzIHuSYPPlJwaO2q6SfsiuX V4zWw1NZXR1G1oQe6TZN7brWRe2FpqgfDI70VnzLnb90yWDxGAkyMtcNp+t6alUo 5XggAYrnJVRPBZLkGC6JwoRudjILb+wj6IaC4Bh06XIZunaZGCqZwlmtZ8v/qYDq eMilB0xb+rHNeciqogsCsjtxd/loZMGBubXTYzty/mEjehYHSWy2f7O/lutA42k9 R3I2oP67tmE= =gHC2 -----END PGP SIGNATURE----- Mon Jan 27 16:10:22 UTC 2025 I: Checking whether the package is not for us Mon Jan 27 16:10:22 UTC 2025 I: Starting 1st build on remote node wbq0-armhf-rb.debian.net. Mon Jan 27 16:10:22 UTC 2025 I: Preparing to do remote build '1' on wbq0-armhf-rb.debian.net. Mon Jan 27 16:24:22 UTC 2025 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 27 04:10:31 -12 2025 I: pbuilder-time-stamp: 1737994231 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbpp-phyl-omics_2.4.1-7.dsc] I: copying [./libbpp-phyl-omics_2.4.1.orig.tar.gz] I: copying [./libbpp-phyl-omics_2.4.1-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbpp-phyl-omics_2.4.1-7.dsc: unsupported subcommand dpkg-source: info: extracting libbpp-phyl-omics in libbpp-phyl-omics-2.4.1 dpkg-source: info: unpacking libbpp-phyl-omics_2.4.1.orig.tar.gz dpkg-source: info: unpacking libbpp-phyl-omics_2.4.1-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying unforce-cxxflags.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4875/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=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='54533576ecd2419385bd690f2ff6a710' 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='4875' 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.1ONn8a3b/pbuilderrc_swyE --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1ONn8a3b/b1 --logfile b1/build.log libbpp-phyl-omics_2.4.1-7.dsc' SUDO_GID='113' SUDO_UID='107' 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 wbq0 6.1.0-30-armmp #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4875/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: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), cmake, d-shlibs (>= 0.106~), libbpp-phyl-dev, libbpp-seq-omics-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 ... 19568 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.106~); however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libbpp-phyl-dev; however: Package libbpp-phyl-dev is not installed. pbuilder-satisfydepends-dummy depends on libbpp-seq-omics-dev; however: Package libbpp-seq-omics-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} cmake{a} cmake-data{a} d-shlibs{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} libarchive13t64{a} libbpp-core-dev{a} libbpp-core4t64{a} libbpp-phyl-dev{a} libbpp-phyl12t64{a} libbpp-seq-dev{a} libbpp-seq-omics-dev{a} libbpp-seq-omics3t64{a} libbpp-seq12t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libicu72{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 41.2 MB of archives. After unpacking 181 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libproc2-0 armhf 2:4.0.4-7 [56.3 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf procps armhf 2:4.0.4-7 [866 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.23.1-1 [238 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.4-1 [84.6 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf automake all 1:1.17-1 [861 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf autopoint all 0.23.1-1 [770 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf cmake-data all 3.31.4-2 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libarchive13t64 armhf 3.7.4-1.1 [306 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-4 [30.3 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-4 [75.8 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 27 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-4 [285 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-4 [116 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libidn2-0 armhf 2.3.7-2+b1 [125 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8+b1 [18.6 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8+b1 [50.6 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libldap2 armhf 2.6.9+dfsg-1 [167 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libffi8 armhf 3.4.6-1 [20.0 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libtasn1-6 armhf 4.19.0-3+b3 [43.9 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libgnutls30t64 armhf 3.8.8-2 [1370 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.11.1-1+b1 [304 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf libjsoncpp26 armhf 1.9.6-3 [69.9 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf librhash1 armhf 1.4.5-1 [143 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libuv1t64 armhf 1.48.0-7 [134 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf cmake armhf 3.31.4-2 [5912 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf d-shlibs all 0.109 [11.1 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.24.1 [90.9 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libtool all 2.5.4-2 [539 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 55 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.23.1-1 [1560 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf debhelper all 13.24.1 [920 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libbpp-core4t64 armhf 2.4.1-13+b1 [533 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libbpp-core-dev armhf 2.4.1-13+b1 [957 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libbpp-seq12t64 armhf 2.4.1-13 [454 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libbpp-phyl12t64 armhf 2.4.1-11+b1 [1472 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libbpp-seq-dev armhf 2.4.1-13 [747 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libbpp-phyl-dev armhf 2.4.1-11+b1 [3096 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libbpp-seq-omics3t64 armhf 2.4.1-12 [205 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libbpp-seq-omics-dev armhf 2.4.1-12 [391 kB] Fetched 41.2 MB in 4s (11.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0: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 ... 19568 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-7_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-7_armhf.deb ... Unpacking procps (2:4.0.4-7) ... Selecting previously unselected package sensible-utils. 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Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libbpp-seq-omics-dev:armhf (2.4.1-12) ... Setting up libcurl4t64:armhf (8.11.1-1+b1) ... Setting up debhelper (13.24.1) ... Setting up cmake (3.31.4-2) ... Processing triggers for libc-bin (2.40-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/ && 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 > ../libbpp-phyl-omics_2.4.1-7_source.changes dpkg-buildpackage: info: source package libbpp-phyl-omics dpkg-buildpackage: info: source version 2.4.1-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf .. CMake Deprecation Warning at CMakeLists.txt:8 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- bpp-core 4.1.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -- includes: /usr/include -- bpp-seq 12.0.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 -- includes: /usr/include -- bpp-seq-omics 3.0.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.so.3.0.0 -- includes: /usr/include -- bpp-phyl 12.0.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 -- includes: /usr/include -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done (3.3s) -- Generating done (0.1s) 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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf dh_auto_build cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-omics-2.4.1 -B/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/bpp-phyl-omics-static.dir/build.make src/CMakeFiles/bpp-phyl-omics-static.dir/depend make -f src/CMakeFiles/bpp-phyl-omics-shared.dir/build.make src/CMakeFiles/bpp-phyl-omics-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-omics-2.4.1 /build/reproducible-path/libbpp-phyl-omics-2.4.1/src /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-omics-static.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-omics-2.4.1 /build/reproducible-path/libbpp-phyl-omics-2.4.1/src /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src/CMakeFiles/bpp-phyl-omics-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/bpp-phyl-omics-static.dir/build.make src/CMakeFiles/bpp-phyl-omics-static.dir/build make -f src/CMakeFiles/bpp-phyl-omics-shared.dir/build.make src/CMakeFiles/bpp-phyl-omics-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' [ 5%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o [ 15%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o [ 15%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong 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-I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp [ 45%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp [ 50%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp [ 55%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp [ 60%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp [ 65%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp [ 70%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp [ 75%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp [ 80%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp [ 85%] Linking CXX shared library libbpp-phyl-omics.so cd 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"CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o" /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.so.3.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_symlink_library libbpp-phyl-omics.so.3.0.0 libbpp-phyl-omics.so.3 libbpp-phyl-omics.so make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' [ 85%] Built target bpp-phyl-omics-shared [ 90%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp [ 95%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o -c /build/reproducible-path/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp [100%] Linking CXX static library libbpp-phyl-omics.a cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/bpp-phyl-omics-static.dir/cmake_clean_target.cmake cd /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-phyl-omics-static.dir/link.txt --verbose=1 /usr/bin/ar qc libbpp-phyl-omics.a "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o" /usr/bin/ranlib libbpp-phyl-omics.a make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' [100%] Built target bpp-phyl-omics-static make[2]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-omics-2.4.1 -B/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl-omics/bpp-phyl-omics-config.cmake -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl-omics/bpp-phyl-omics-config-version.cmake -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.a -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3 -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/CountClustersMafStatistics.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/AbstractPhylogenyReconstructionMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl-omics/bpp-phyl-omics-targets.cmake -- Installing: /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl-omics/bpp-phyl-omics-targets-none.cmake make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1' dh_install d-shlibmove --commit \ --t64 \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ --movedev debian/tmp/usr/lib/*/cmake usr/lib/arm-linux-gnueabihf \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libbpp-core-dev package exists. --> libbpp-phyl-dev package exists. --> libbpp-seq-dev package exists. --> libbpp-seq-omics-dev package exists. set -e install -d -m 755 debian/libbpp-phyl-omics-dev/usr/lib/arm-linux-gnueabihf install -d -m 755 debian/libbpp-phyl-omics3t64/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.a debian/libbpp-phyl-omics-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so debian/libbpp-phyl-omics-dev/usr/lib/arm-linux-gnueabihf mv /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3 debian/libbpp-phyl-omics3t64/usr/lib/arm-linux-gnueabihf mv /build/reproducible-path/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 debian/libbpp-phyl-omics3t64/usr/lib/arm-linux-gnueabihf PKGDEV=libbpp-phyl-omics-dev PKGSHL=libbpp-phyl-omics3t64 install -d -m 755 debian/libbpp-phyl-omics-dev/usr/include mv debian/tmp/usr/include/Bpp debian/libbpp-phyl-omics-dev/usr/include install -d -m 755 debian/libbpp-phyl-omics-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/cmake debian/libbpp-phyl-omics-dev/usr/lib/arm-linux-gnueabihf make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-omics-2.4.1' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libbpp-phyl-omics3t64/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 found in none of the libraries dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbpp-phyl-omics3t64' in '../libbpp-phyl-omics3t64_2.4.1-7_armhf.deb'. dpkg-deb: building package 'libbpp-phyl-omics-dev' in '../libbpp-phyl-omics-dev_2.4.1-7_armhf.deb'. dpkg-deb: building package 'libbpp-phyl-omics3t64-dbgsym' in '../libbpp-phyl-omics3t64-dbgsym_2.4.1-7_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-phyl-omics_2.4.1-7_armhf.buildinfo dpkg-genchanges --build=binary -O../libbpp-phyl-omics_2.4.1-7_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/4875 and its subdirectories I: Current time: Mon Jan 27 04:24:12 -12 2025 I: pbuilder-time-stamp: 1737995052 Mon Jan 27 16:24:24 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Mon Jan 27 16:24:24 UTC 2025 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Mon Jan 27 16:27:09 UTC 2025 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Mon Jan 27 16:27:11 UTC 2025 I: libbpp-phyl-omics_2.4.1-7_armhf.changes: Format: 1.8 Date: Fri, 05 Jul 2024 18:10:01 +0200 Source: libbpp-phyl-omics Binary: libbpp-phyl-omics-dev libbpp-phyl-omics3t64 libbpp-phyl-omics3t64-dbgsym Architecture: armhf Version: 2.4.1-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-phyl-omics-dev - Bio++ Phylogenetics library: genomics components (development fil libbpp-phyl-omics3t64 - Bio++ Phylogenetics library: genomics components Closes: 1075149 Changes: libbpp-phyl-omics (2.4.1-7) unstable; urgency=medium . * Since every GCC version bump ends up in a bug caused by the need to update symbols files we stop providing symbols for this library Closes: 1075149 * lintian-override for no-symbols-control-file * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: 7b9330c29fb776d77f69bef4d789a59c43bd2a0d 143572 libbpp-phyl-omics-dev_2.4.1-7_armhf.deb dbe8cc6ebebdacf39b5dfbbc78468700a9c3d064 2708448 libbpp-phyl-omics3t64-dbgsym_2.4.1-7_armhf.deb 3bb0fa30dc5ab90706b799b38ca23efff8a5aeef 63004 libbpp-phyl-omics3t64_2.4.1-7_armhf.deb 0e7d988c2c6d867739323b0f5e4be124fe400604 6853 libbpp-phyl-omics_2.4.1-7_armhf.buildinfo Checksums-Sha256: 87be401cf61a2ef250514b886b1aef1b02f15f0b610feba09e8312f2ae3007d3 143572 libbpp-phyl-omics-dev_2.4.1-7_armhf.deb 9a6a4f6c97cb068db15f8b497b30bb84f33b4a62c16ee914678c68e201456cc5 2708448 libbpp-phyl-omics3t64-dbgsym_2.4.1-7_armhf.deb 61c8910d9f741de6039e8161dd0907b327e351d9d9e8a4e8bf87aad3eb042851 63004 libbpp-phyl-omics3t64_2.4.1-7_armhf.deb cd03bcdef2c563926753bfcd9d22fd4f602ab1a465c71b3e9003e3b5430a6c91 6853 libbpp-phyl-omics_2.4.1-7_armhf.buildinfo Files: 05723c6a9c33fc1fd48319aecd0c1047 143572 libdevel optional libbpp-phyl-omics-dev_2.4.1-7_armhf.deb 5f2690c7017f17ecece844460c4595df 2708448 debug optional libbpp-phyl-omics3t64-dbgsym_2.4.1-7_armhf.deb 21312b03f6d39244753aa78d966fca6d 63004 libs optional libbpp-phyl-omics3t64_2.4.1-7_armhf.deb 153f1e8401fca5654ed8ce46d13e69d1 6853 science optional libbpp-phyl-omics_2.4.1-7_armhf.buildinfo Mon Jan 27 16:27:15 UTC 2025 I: diffoscope 286 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_10-6991.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.1ONn8a3b/libbpp-phyl-omics_2.4.1-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.1ONn8a3b/libbpp-phyl-omics_2.4.1-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.1ONn8a3b/libbpp-phyl-omics_2.4.1-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.1ONn8a3b/b1/libbpp-phyl-omics_2.4.1-7_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.1ONn8a3b/b2/libbpp-phyl-omics_2.4.1-7_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.049s) 0.049s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 268ms CPU time consumed: 225ms Mon Jan 27 16:27:16 UTC 2025 I: diffoscope 286 found no differences in the changes files, and a .buildinfo file also exists. Mon Jan 27 16:27:16 UTC 2025 I: libbpp-phyl-omics from unstable built successfully and reproducibly on armhf. Mon Jan 27 16:27:17 UTC 2025 I: Submitting .buildinfo files to external archives: Mon Jan 27 16:27:17 UTC 2025 I: Submitting 8.0K b1/libbpp-phyl-omics_2.4.1-7_armhf.buildinfo.asc Mon Jan 27 16:27:21 UTC 2025 I: Submitting 8.0K b2/libbpp-phyl-omics_2.4.1-7_armhf.buildinfo.asc Mon Jan 27 16:27:25 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 27 16:27:25 UTC 2025 I: Done submitting .buildinfo files. Mon Jan 27 16:27:25 UTC 2025 I: Removing signed libbpp-phyl-omics_2.4.1-7_armhf.buildinfo.asc files: removed './b1/libbpp-phyl-omics_2.4.1-7_armhf.buildinfo.asc' removed './b2/libbpp-phyl-omics_2.4.1-7_armhf.buildinfo.asc'