Thu May 25 14:33:55 UTC 2023 I: starting to build libbpp-phyl-omics/bookworm/armhf on jenkins on '2023-05-25 14:33' Thu May 25 14:33:55 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_35/2942/console.log Thu May 25 14:33:55 UTC 2023 I: Downloading source for bookworm/libbpp-phyl-omics=2.4.1-4 --2023-05-25 14:33:55-- http://cdn-fastly.deb.debian.org/debian/pool/main/libb/libbpp-phyl-omics/libbpp-phyl-omics_2.4.1-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2233 (2.2K) [text/prs.lines.tag] Saving to: ‘libbpp-phyl-omics_2.4.1-4.dsc’ 0K .. 100% 186M=0s 2023-05-25 14:33:55 (186 MB/s) - ‘libbpp-phyl-omics_2.4.1-4.dsc’ saved [2233/2233] Thu May 25 14:33:55 UTC 2023 I: libbpp-phyl-omics_2.4.1-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbpp-phyl-omics Binary: libbpp-phyl-omics-dev, libbpp-phyl-omics3 Architecture: any Version: 2.4.1-4 Maintainer: Debian Med Packaging Team Uploaders: Julien Dutheil , Andreas Tille Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Standards-Version: 4.6.1 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: debhelper-compat (= 13), cmake, d-shlibs, libbpp-phyl-dev, libbpp-seq-omics-dev Package-List: libbpp-phyl-omics-dev deb libdevel optional arch=any libbpp-phyl-omics3 deb libs optional arch=any Checksums-Sha1: b3132c35963eec7890514c1766b6c13f5c661a31 48482 libbpp-phyl-omics_2.4.1.orig.tar.gz 468bc84169230ee10cc31ad9f0215ff03be88c4a 13860 libbpp-phyl-omics_2.4.1-4.debian.tar.xz Checksums-Sha256: fb0908422e59c71065db874e68d5c71acddf66d8a51776f7e04a5f8d5f0f6577 48482 libbpp-phyl-omics_2.4.1.orig.tar.gz ab0acf1e0c2ee6f570d61b4a178e490137470b546a4b82f50173ee97de544290 13860 libbpp-phyl-omics_2.4.1-4.debian.tar.xz Files: 7c1c1d06e0c0ff61ddecc7fcc4064f51 48482 libbpp-phyl-omics_2.4.1.orig.tar.gz 21d33603fc855c1a9ba6438c611daa86 13860 libbpp-phyl-omics_2.4.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmN3gM8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEJxRAAjQO9YKKdYUS77ER/GPhFoQJRfnvE0cG7 qcGLbgYuupPsePONmPSuP00imwrgx2bBq5/kfPF6djnWQHbw5LL3kxM3sE+yZXoJ 9rgkpeaJlE+eXhpHSXDiuvEUt7N7E8z0knALi5UDUlniaYfK2zOtZ5GdWfMwJqtY UtZGpbY59Nk2YETq6eT6cy6tRsQj2ZMC5DraHVTWIjADUB5NmFr5P08G2QwX9nCP F6UqBBHqcrSFuGnht6ZllFDvNcJ4KA716cVtKyhoVUB7jvtoJuRaMnAzjEglGJVr 1HHW0otnBXQUlXjArXyDoElmLXmqUJ+ss5TUrAvJ6sGrvKg2y4CrTF3CD4Hov9bw wwyuJMew7qyC/tZXLR95Me4hyQY4n8+4pTKmzSWcsjFbfq/tY+OLKYuGlTzdyB2R prykgudi8j/i+eLVxAnEOJIPgDZV+z+F1KwLjo4U8rswZQTurIfgDW5iK8J38MdD 7XNTl4p/c5iza1IWcNMogOxxx6RXQkathdasxk/IkUQbRVmms/sc80kdsoCo1/VS RuXXwNr1iFCNkHIZ3+hE4mPtHRqq20jZDb3fpXhEM6n6x8B+lg1pZQE9oSrWA6Ok X/IPxK0PTCqszSkGvkFP7oyT5mfbhU2/zzoniXCQ6dFdSMiDscdU6slgCqcnF4rn trwSia+GFdc= =cHMa -----END PGP SIGNATURE----- Thu May 25 14:33:55 UTC 2023 I: Checking whether the package is not for us Thu May 25 14:33:55 UTC 2023 I: Starting 1st build on remote node jtx1c-armhf-rb.debian.net. Thu May 25 14:33:55 UTC 2023 I: Preparing to do remote build '1' on jtx1c-armhf-rb.debian.net. Thu May 25 14:37:28 UTC 2023 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 25 02:34:01 -12 2023 I: pbuilder-time-stamp: 1685025241 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_2.4.1-4.dsc] I: copying [./libbpp-phyl-omics_2.4.1.orig.tar.gz] I: copying [./libbpp-phyl-omics_2.4.1-4.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Nov 18 00:55:43 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libbpp-phyl-omics_2.4.1-4.dsc: no acceptable signature found 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_2.4.1-4.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/2249/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='1b380a43ca014ad2a558a8c98deb8482' 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='2249' 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.l4g2pOcJ/pbuilderrc_oa6F --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.l4g2pOcJ/b1 --logfile b1/build.log libbpp-phyl-omics_2.4.1-4.dsc' SUDO_GID='114' SUDO_UID='108' 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 jtx1c 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2249/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, d-shlibs, 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 ... 19326 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; 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} libarchive13{a} libbpp-core-dev{a} libbpp-core4{a} libbpp-phyl-dev{a} libbpp-phyl12{a} libbpp-seq-dev{a} libbpp-seq-omics-dev{a} libbpp-seq-omics3{a} libbpp-seq12{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 34.7 MB of archives. After unpacking 159 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libarchive13 armhf 3.6.2-1 [299 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf librhash0 armhf 1.4.3-3 [146 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libuv1 armhf 1.44.2-1 [126 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf cmake-data all 3.25.1-1 [2026 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf cmake armhf 3.25.1-1 [4263 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf d-shlibs all 0.104 [18.6 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 42 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 44 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libbpp-core4 armhf 2.4.1-9 [501 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libbpp-core-dev armhf 2.4.1-9 [943 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libbpp-seq12 armhf 2.4.1-9 [420 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libbpp-phyl12 armhf 2.4.1-8 [1384 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libbpp-seq-dev armhf 2.4.1-9 [733 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libbpp-phyl-dev armhf 2.4.1-8 [3095 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libbpp-seq-omics3 armhf 2.4.1-9 [190 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libbpp-seq-omics-dev armhf 2.4.1-9 [382 kB] Fetched 34.7 MB in 7s (5138 kB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19326 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.2-3_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.2-3_armhf.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/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_2.4.1-4_source.changes dpkg-buildpackage: info: source package libbpp-phyl-omics dpkg-buildpackage: info: source version 2.4.1-4 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 debian/rules:40: warning: overriding recipe for target 'override_dh_makeshlibs' debian/rules:16: warning: ignoring old recipe for target 'override_dh_makeshlibs' dh clean dh_clean debian/rules binary debian/rules:40: warning: overriding recipe for target 'override_dh_makeshlibs' debian/rules:16: warning: ignoring old recipe for target 'override_dh_makeshlibs' dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-arm-linux-gnueabihf && 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 < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 12.2.0 -- 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 -- Generating done 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/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libbpp-phyl-omics-2.4.1 -B/build/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-omics-2.4.1 /build/libbpp-phyl-omics-2.4.1/src /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src /build/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-omics-2.4.1 /build/libbpp-phyl-omics-2.4.1/src /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src /build/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/bpp-phyl-omics-shared.dir/build.make src/CMakeFiles/bpp-phyl-omics-shared.dir/build make -f src/CMakeFiles/bpp-phyl-omics-static.dir/build.make src/CMakeFiles/bpp-phyl-omics-static.dir/build make[3]: Entering directory '/build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' [ 15%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -c /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o -c /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 20%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o -c /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp [ 25%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o -c /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp [ 30%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o -c /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp [ 35%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp [ 40%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o -MF CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o.d -o CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o -c /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp [ 45%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp [ 50%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 55%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp [ 65%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 70%] Building CXX object src/CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -Dbpp_phyl_omics_shared_EXPORTS -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 75%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp [ 80%] Linking CXX shared library libbpp-phyl-omics.so cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-phyl-omics-shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libbpp-phyl-omics.so.3 -o libbpp-phyl-omics.so.3.0.0 "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp.o" "CMakeFiles/bpp-phyl-omics-shared.dir/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp.o" "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/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' [ 80%] Built target bpp-phyl-omics-shared [ 85%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 90%] Building CXX object src/CMakeFiles/bpp-phyl-omics-static.dir/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp.o cd /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -I/build/libbpp-phyl-omics-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-omics-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h:43, from /build/libbpp-phyl-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp:40: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [100%] Linking CXX static library libbpp-phyl-omics.a cd /build/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/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' [100%] Built target bpp-phyl-omics-static make[2]: Leaving directory '/build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/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/libbpp-phyl-omics-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libbpp-phyl-omics-2.4.1 -B/build/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/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/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl-omics/bpp-phyl-omics-config.cmake -- Installing: /build/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/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.a -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3 -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/CountClustersMafStatistics.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/AbstractPhylogenyReconstructionMafIterator.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h -- Installing: /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/bpp-phyl-omics/bpp-phyl-omics-targets.cmake -- Installing: /build/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/libbpp-phyl-omics-2.4.1/obj-arm-linux-gnueabihf' debian/rules override_dh_install make[1]: Entering directory '/build/libbpp-phyl-omics-2.4.1' debian/rules:40: warning: overriding recipe for target 'override_dh_makeshlibs' debian/rules:16: warning: ignoring old recipe for target 'override_dh_makeshlibs' dh_install d-shlibmove --commit \ --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-omics3/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/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3 debian/libbpp-phyl-omics3/usr/lib/arm-linux-gnueabihf mv /build/libbpp-phyl-omics-2.4.1/debian/tmp/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 debian/libbpp-phyl-omics3/usr/lib/arm-linux-gnueabihf PKGDEV=libbpp-phyl-omics-dev PKGSHL=libbpp-phyl-omics3 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/libbpp-phyl-omics-2.4.1' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debian/rules override_dh_makeshlibs make[1]: Entering directory '/build/libbpp-phyl-omics-2.4.1' debian/rules:40: warning: overriding recipe for target 'override_dh_makeshlibs' debian/rules:16: warning: ignoring old recipe for target 'override_dh_makeshlibs' dh_makeshlibs 2>&1 | tee > ../dh_makeshlibs.diff make[1]: Leaving directory '/build/libbpp-phyl-omics-2.4.1' dh_shlibdeps -a dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libbpp-phyl-omics3/usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 found in none of the libraries dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package libbpp-phyl-omics-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libbpp-phyl-omics-dev' in '../libbpp-phyl-omics-dev_2.4.1-4_armhf.deb'. dpkg-deb: building package 'libbpp-phyl-omics3' in '../libbpp-phyl-omics3_2.4.1-4_armhf.deb'. dpkg-deb: building package 'libbpp-phyl-omics3-dbgsym' in '../libbpp-phyl-omics3-dbgsym_2.4.1-4_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-phyl-omics_2.4.1-4_armhf.buildinfo dpkg-genchanges --build=binary -O../libbpp-phyl-omics_2.4.1-4_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/2249 and its subdirectories I: Current time: Thu May 25 02:37:20 -12 2023 I: pbuilder-time-stamp: 1685025440 Thu May 25 14:37:30 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt32c-armhf-rb.debian.net. Thu May 25 14:37:30 UTC 2023 I: Preparing to do remote build '2' on virt32c-armhf-rb.debian.net. Thu May 25 14:48:23 UTC 2023 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net. Thu May 25 14:48:25 UTC 2023 I: libbpp-phyl-omics_2.4.1-4_armhf.changes: Format: 1.8 Date: Fri, 18 Nov 2022 12:59:33 +0100 Source: libbpp-phyl-omics Binary: libbpp-phyl-omics-dev libbpp-phyl-omics3 libbpp-phyl-omics3-dbgsym Architecture: armhf Version: 2.4.1-4 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-omics3 - Bio++ Phylogenetics library: genomics components Changes: libbpp-phyl-omics (2.4.1-4) unstable; urgency=medium . * Fix watch file * Standards-Version: 4.6.1 (routine-update) * Update symbols file Checksums-Sha1: 4aef27bc14e1712741fc890b4bd88c6a69f9827c 145744 libbpp-phyl-omics-dev_2.4.1-4_armhf.deb d87ef259f1cd3c06d05a91f5f72ad67570d170f2 2667272 libbpp-phyl-omics3-dbgsym_2.4.1-4_armhf.deb e29cc9e6d72ce0b103cc5cc08bf9014bc4c50109 63220 libbpp-phyl-omics3_2.4.1-4_armhf.deb c50c81efa0eb6184000c27832b389082ba104eda 6588 libbpp-phyl-omics_2.4.1-4_armhf.buildinfo Checksums-Sha256: 910462e5c8eb5eced534d34e18617a42f8ba9af5457b00f55f964846d22b9ccb 145744 libbpp-phyl-omics-dev_2.4.1-4_armhf.deb 05e3657de1625df8b2d139a8386099bc45715573c61c23650fafd8b1fa9be2f3 2667272 libbpp-phyl-omics3-dbgsym_2.4.1-4_armhf.deb 2122890dbfd2ce6e7b54a858ccba196279413fd1c44b9dcbbf63f5b48bc1b5f3 63220 libbpp-phyl-omics3_2.4.1-4_armhf.deb 550e5effa1c45a89ed63234790290a9907be560b40250735f25797857b327016 6588 libbpp-phyl-omics_2.4.1-4_armhf.buildinfo Files: d506a6780ba1100deb42915e5de8c76d 145744 libdevel optional libbpp-phyl-omics-dev_2.4.1-4_armhf.deb ed2e5cbccd570dab96a290448466cc50 2667272 debug optional libbpp-phyl-omics3-dbgsym_2.4.1-4_armhf.deb beb6dfa8b21f5d0b7ce95ac9b1e5e3ac 63220 libs optional libbpp-phyl-omics3_2.4.1-4_armhf.deb 09fe9e81fc011631c732bfdbcc210eec 6588 science optional libbpp-phyl-omics_2.4.1-4_armhf.buildinfo Thu May 25 14:48:27 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.l4g2pOcJ/libbpp-phyl-omics_2.4.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.l4g2pOcJ/libbpp-phyl-omics_2.4.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.l4g2pOcJ/libbpp-phyl-omics_2.4.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.l4g2pOcJ/b1/libbpp-phyl-omics_2.4.1-4_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.l4g2pOcJ/b2/libbpp-phyl-omics_2.4.1-4_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 abc.DotChangesFile ## main (total time: 0.330s) 0.330s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.044s) 0.044s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Thu May 25 14:48:27 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Thu May 25 14:48:27 UTC 2023 I: libbpp-phyl-omics from bookworm built successfully and reproducibly on armhf. Thu May 25 14:48:29 UTC 2023 I: Submitting .buildinfo files to external archives: Thu May 25 14:48:29 UTC 2023 I: Submitting 8.0K b1/libbpp-phyl-omics_2.4.1-4_armhf.buildinfo.asc Thu May 25 14:48:30 UTC 2023 I: Submitting 8.0K b2/libbpp-phyl-omics_2.4.1-4_armhf.buildinfo.asc Thu May 25 14:48:31 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 25 14:48:31 UTC 2023 I: Done submitting .buildinfo files. Thu May 25 14:48:31 UTC 2023 I: Removing signed libbpp-phyl-omics_2.4.1-4_armhf.buildinfo.asc files: removed './b1/libbpp-phyl-omics_2.4.1-4_armhf.buildinfo.asc' removed './b2/libbpp-phyl-omics_2.4.1-4_armhf.buildinfo.asc'