Tue Aug 10 16:53:10 UTC 2021 I: starting to build phyml/bullseye/armhf on jenkins on '2021-08-10 16:53' Tue Aug 10 16:53:10 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_25/4071/console.log Tue Aug 10 16:53:10 UTC 2021 I: Downloading source for bullseye/phyml=3:3.3.20200621-1 --2021-08-10 16:53:10-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/phyml/phyml_3.3.20200621-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2094 (2.0K) Saving to: ‘phyml_3.3.20200621-1.dsc’ 0K .. 100% 221M=0s 2021-08-10 16:53:11 (221 MB/s) - ‘phyml_3.3.20200621-1.dsc’ saved [2094/2094] Tue Aug 10 16:53:11 UTC 2021 I: phyml_3.3.20200621-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: phyml Binary: phyml Architecture: any Version: 3:3.3.20200621-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Kevin Murray Homepage: http://www.atgc-montpellier.fr/phyml Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/phyml Vcs-Git: https://salsa.debian.org/med-team/phyml.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), pkg-config, libopenmpi-dev, chrpath Package-List: phyml deb science optional arch=any Checksums-Sha1: df6cc658a1733806b9c467e82f152b2fff6cd5bd 2235154 phyml_3.3.20200621.orig.tar.gz 5c941bc6c685697b7bb553250de3781f20437df5 17296 phyml_3.3.20200621-1.debian.tar.xz Checksums-Sha256: a8243923ee08c74cab609a4b086ade66c6156fc2b24450e2a500108dc644c867 2235154 phyml_3.3.20200621.orig.tar.gz 4a634ce483f68a707ddbc8a215cf5b2701e3671dbf7bf8f6dcff3b9376e6b2a7 17296 phyml_3.3.20200621-1.debian.tar.xz Files: 12622e111c388bcb16696660033143b5 2235154 phyml_3.3.20200621.orig.tar.gz 877a070edeb3e61e0eab3a92afdeff3c 17296 phyml_3.3.20200621-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl8YmFsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFmVQ/+Lj1Hoz28KFtMP7AGTkdpYA8hnJlh10wT p3JT2Y+jKpmNU6ZTSVlKDE6Ddre4nvHjWij1A/fNv695inuWuOFe+3/fGBXtxd99 JiZXOYnaOKni7VXPj4Auytm0dEkFyZXvQHytcwaJf7FD4zVFsOPbx6x9LC7Y4qEo JjnFidY2I0Dn2FidPLF39HXt6ms9pVyn2h89bhMfBT8zUpe9v2oP8JrjaEcYvQnP EFC2Rc5tPrFKVHp+e9iRYVFEi5r1y8X7IcPO6vDgwRulK2ln9PCvVF23qxErS8Yh Z7iN41Fylm7vuqZplzkCwg6C0uwhaVC90v1Nz0ny95blsbrsJTecm/EBSYi1BOR6 JT6SQS4IisyiK/7yZB2Kr3X/SXtx88/VXB0GcQYRFr83g1/pEUJ8BUjBTKoyl7uW 9g0eNJtTIfu33lZM3iWjrXp2WxJ6OQU4XRYy86r8WLP3s+rsOY+cFIEhDyxPlwny 3lCX3QnTqq4U3uLeJ3ewxvFEi/i2+unm0AgNS4cAD8ihP2jqwubDvGmfKBFMVelr Fm4K0LgA1MUU1y9nOeFFdsTXd17/0E0O2XE13h/Ffjoyz1QCMXjQbmepfW9sdyvQ RFdjkTO5aclkYMzglM9h8jeRfusw4jl+DX8aE4wVirLDE69DesR7e6TNBbRJqo7Z 4wHLFHtr9/0= =Ssyh -----END PGP SIGNATURE----- Tue Aug 10 16:53:11 UTC 2021 I: Checking whether the package is not for us Tue Aug 10 16:53:11 UTC 2021 I: Starting 1st build on remote node virt32c-armhf-rb.debian.net. Tue Aug 10 16:53:11 UTC 2021 I: Preparing to do remote build '1' on virt32c-armhf-rb.debian.net. Tue Aug 10 16:56:51 UTC 2021 I: Deleting $TMPDIR on virt32c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Aug 10 04:53:16 -12 2021 I: pbuilder-time-stamp: 1628614396 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [phyml_3.3.20200621-1.dsc] I: copying [./phyml_3.3.20200621.orig.tar.gz] I: copying [./phyml_3.3.20200621-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.8w9a8HYZ/trustedkeys.kbx': General error gpgv: Signature made Wed Jul 22 07:49:47 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phyml_3.3.20200621-1.dsc dpkg-source: info: extracting phyml in phyml-3.3.20200621 dpkg-source: info: unpacking phyml_3.3.20200621.orig.tar.gz dpkg-source: info: unpacking phyml_3.3.20200621-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sse_only_if_supported.patch dpkg-source: info: applying no-stdc++.patch dpkg-source: info: applying no-configure-ac-date.patch dpkg-source: info: applying fix_declaration_of_temp.patch dpkg-source: info: applying fix_wrong_initialisation_of_array.patch dpkg-source: info: applying no-march-native.patch dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14924/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,-fixfilepath parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='ff44931bae054b6590cf6c16286ba0a0' 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='14924' 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/tmp.HyyWoYf6g0/pbuilderrc_lAv2 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.HyyWoYf6g0/b1 --logfile b1/build.log phyml_3.3.20200621-1.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://10.0.0.15:8000/' I: uname -a Linux virt32c 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 9 21:24 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/14924/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), pkg-config, libopenmpi-dev, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 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 pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath 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} chrpath{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-10{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcbor0{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-10-dev{a} libgfortran5{a} libglib2.0-0{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu67{a} libjs-jquery{a} libjs-jquery-ui{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix-dev{a} libpmix2{a} librdmacm1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 37.2 MB of archives. After unpacking 125 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libmd0 armhf 1.0.3-3 [27.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf libbsd0 armhf 0.11.3-1 [103 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf libedit2 armhf 3.1-20191231-2+b1 [81.1 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.6 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf libfido2-1 armhf 1.6.0-2 [48.0 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf openssh-client armhf 1:8.4p1-5 [842 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf chrpath armhf 0.16-2+b1 [15.9 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libgfortran5 armhf 10.2.1-6 [237 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libgfortran-10-dev armhf 10.2.1-6 [289 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf gfortran-10 armhf 10.2.1-6 [7123 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libnl-3-200 armhf 3.4.0-1+b1 [55.5 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libnl-route-3-200 armhf 3.4.0-1+b1 [136 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libibverbs1 armhf 33.2-1 [53.0 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf ibverbs-providers armhf 33.2-1 [25.4 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [169 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [127 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [101 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.6 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf libevent-dev armhf 2.1.12-stable-1 [296 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf librdmacm1 armhf 33.2-1 [60.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf libfabric1 armhf 1.11.0-2 [319 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf libhwloc15 armhf 2.4.1+dfsg-1 [125 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf libnuma1 armhf 2.0.12-1+b1 [22.7 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf libnuma-dev armhf 2.0.12-1+b1 [37.0 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf libltdl7 armhf 2.4.6-15 [388 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf libltdl-dev armhf 2.4.6-15 [159 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf libhwloc-dev armhf 2.4.1+dfsg-1 [208 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 64 http://deb.debian.org/debian bullseye/main armhf libxcb1 armhf 1.14-3 [136 kB] Get: 65 http://deb.debian.org/debian bullseye/main armhf libx11-data all 2:1.7.2-1 [311 kB] Get: 66 http://deb.debian.org/debian bullseye/main armhf libx11-6 armhf 2:1.7.2-1 [713 kB] Get: 67 http://deb.debian.org/debian bullseye/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf libxnvctrl0 armhf 460.91.03-1 [25.8 kB] Get: 69 http://deb.debian.org/debian bullseye/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.7 kB] Get: 70 http://deb.debian.org/debian bullseye/main armhf libhwloc-plugins armhf 2.4.1+dfsg-1 [19.7 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf libnl-3-dev armhf 3.4.0-1+b1 [97.1 kB] Get: 72 http://deb.debian.org/debian bullseye/main armhf libnl-route-3-dev armhf 3.4.0-1+b1 [160 kB] Get: 73 http://deb.debian.org/debian bullseye/main armhf libibverbs-dev armhf 33.2-1 [183 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get: 76 http://deb.debian.org/debian bullseye/main armhf libpmix2 armhf 4.0.0-4.1 [487 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf libopenmpi3 armhf 4.1.0-10 [1831 kB] Get: 78 http://deb.debian.org/debian bullseye/main armhf openmpi-common all 4.1.0-10 [179 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Get: 80 http://deb.debian.org/debian bullseye/main armhf libpmix-dev armhf 4.0.0-4.1 [618 kB] Get: 81 http://deb.debian.org/debian bullseye/main armhf openmpi-bin armhf 4.1.0-10 [206 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf libopenmpi-dev armhf 4.1.0-10 [1143 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Fetched 37.2 MB in 5s (6994 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.66.8-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.3.4) ... Setting up libcbor0:armhf (0.5.0+dfsg-2) ... Setting up libmagic1:armhf (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libx11-data (2:1.7.2-1) ... Setting up libsigsegv2:armhf (2.13-1) ... Setting up libhwloc15:armhf (2.4.1+dfsg-1) ... Setting up libevent-core-2.1-7:armhf (2.1.12-stable-1) ... Setting up libevent-2.1-7:armhf (2.1.12-stable-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libltdl7:armhf (2.4.6-15) ... Setting up libgfortran5:armhf (10.2.1-6) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ... Setting up libnuma1:armhf (2.0.12-1+b1) ... Setting up libmd0:armhf (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up ocl-icd-libopencl1:armhf (2.2.14-2) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libnl-3-200:armhf (3.4.0-1+b1) ... Setting up openmpi-common (4.1.0-10) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgfortran-10-dev:armhf (10.2.1-6) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libfido2-1:armhf (1.6.0-2) ... Setting up libbsd0:armhf (0.11.3-1) ... Setting up libelf1:armhf (0.183-1) ... Setting up libxml2:armhf (2.9.10+dfsg-6.7) ... Setting up chrpath (0.16-2+b1) ... Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libxdmcp6:armhf (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-1) ... Setting up libxcb1:armhf (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libedit2:armhf (3.1-20191231-2+b1) ... Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnuma-dev:armhf (2.0.12-1+b1) ... Setting up libnl-route-3-200:armhf (3.4.0-1+b1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8) ... Setting up libevent-dev (2.1.12-stable-1) ... Setting up gfortran-10 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libnl-3-dev:armhf (3.4.0-1+b1) ... Setting up groff-base (1.22.4-6) ... Setting up libx11-6:armhf (2:1.7.2-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:armhf (33.2-1) ... Setting up ibverbs-providers:armhf (33.2-1) ... Setting up openssh-client (1:8.4p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:armhf (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:armhf (460.91.03-1) ... Setting up dh-autoreconf (20) ... Setting up libnl-route-3-dev:armhf (3.4.0-1+b1) ... Setting up libltdl-dev:armhf (2.4.6-15) ... Setting up libhwloc-dev:armhf (2.4.1+dfsg-1) ... Setting up librdmacm1:armhf (33.2-1) ... Setting up debhelper (13.3.4) ... Setting up libibverbs-dev:armhf (33.2-1) ... Setting up libhwloc-plugins:armhf (2.4.1+dfsg-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:armhf (4.0.0-4.1) ... Setting up libopenmpi3:armhf (4.1.0-10) ... Setting up libpmix-dev:armhf (4.0.0-4.1) ... Setting up openmpi-bin (4.1.0-10) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:armhf (4.1.0-10) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Processing triggers for libc-bin (2.31-13) ... 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/phyml-3.3.20200621/ && 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 > ../phyml_3.3.20200621-1_source.changes dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20200621-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Shayan Doust dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phyml-3.3.20200621' # save pdf from cleaning mv doc/phyml-manual.pdf . dh_auto_clean mv phyml-manual.pdf doc # remove temporary bin dir for phyml (see above hack) rm -rf debian/bin rm -rf doc/Makefile make[1]: Leaving directory '/build/phyml-3.3.20200621' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/phyml-3.3.20200621' dh_autoreconf --as-needed configure.ac:16: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' make[1]: Leaving directory '/build/phyml-3.3.20200621' debian/rules override_dh_auto_build make[1]: Entering directory '/build/phyml-3.3.20200621' # According to README you need different configure options to get different executables # Here we hack in a full build process for phyml executable # The hack includes saving the documentation from beeing cleaned up mv doc/phyml-manual.pdf . dh_auto_configure ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking dependency style of gcc... (cached) none configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf" checking for log in -lm... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j3 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/phyml-3.3.20200621' make all-recursive make[3]: Entering directory '/build/phyml-3.3.20200621' Making all in src make[4]: Entering directory '/build/phyml-3.3.20200621/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o main.o main.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o utilities.o utilities.c .: Building [phyml]. Version 3.3.3:3.3.20200621-1 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o optimiz.o optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o lk.o lk.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o bionj.o bionj.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o models.o models.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o free.o free.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o help.o help.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o simu.o simu.c utilities.c: In function 'Assign_State_With_Ambiguity': utilities.c:3073:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 3073 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:3073:26: note: directive argument in the range [0, 2147483647] 3073 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from utilities.c:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o eigen.o eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o pars.o pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o alrt.o alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o interface.o interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o cl.o cl.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o spr.o spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o draw.o draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o stats.o stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o rates.o rates.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o mcmc.o mcmc.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o times.o times.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o tiporder.o tiporder.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o io.o io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o make.o make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o nexus.o nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o init.o init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o xml.o xml.c io.c: In function 'Print_Fp_Out': io.c:2315:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2315:43: note: directive argument in the range [1, 2147483647] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from io.h:18, from io.c:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o date.o date.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o sse.o sse.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o avx.o avx.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o tbe.o tbe.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o ancestral.o ancestral.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o mixt.o mixt.c gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o io.o make.o nexus.o init.o xml.o date.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm Done. make[4]: Leaving directory '/build/phyml-3.3.20200621/src' make[4]: Entering directory '/build/phyml-3.3.20200621' make[4]: Leaving directory '/build/phyml-3.3.20200621' make[3]: Leaving directory '/build/phyml-3.3.20200621' make[2]: Leaving directory '/build/phyml-3.3.20200621' # move phyml binary to temporary dir inside debian/ mkdir -p /build/phyml-3.3.20200621/debian/bin mv src/phyml /build/phyml-3.3.20200621/debian/bin/phyml /usr/bin/make distclean make[2]: Entering directory '/build/phyml-3.3.20200621' Making distclean in src make[3]: Entering directory '/build/phyml-3.3.20200621/src' test -z "phyml" || rm -f phyml rm -f *.o rm -f *.tab.c test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/alrt.Po rm -f ./.deps/ancestral.Po rm -f ./.deps/avx.Po rm -f ./.deps/beagle_utils.Po rm -f ./.deps/bionj.Po rm -f ./.deps/checkpoint.Po rm -f ./.deps/cl.Po rm -f ./.deps/date.Po rm -f ./.deps/draw.Po rm -f ./.deps/eigen.Po rm -f ./.deps/free.Po rm -f ./.deps/geo.Po rm -f ./.deps/help.Po rm -f ./.deps/init.Po rm -f ./.deps/interface.Po rm -f ./.deps/invitee.Po rm -f ./.deps/io.Po rm -f ./.deps/lk.Po rm -f ./.deps/main.Po rm -f ./.deps/make.Po rm -f ./.deps/mcmc.Po rm -f ./.deps/mg.Po rm -f ./.deps/mixt.Po rm -f ./.deps/models.Po rm -f ./.deps/nexus.Po rm -f ./.deps/optimiz.Po rm -f ./.deps/pars.Po rm -f ./.deps/phyml_mpi-alrt.Po rm -f ./.deps/phyml_mpi-ancestral.Po rm -f ./.deps/phyml_mpi-avx.Po rm -f ./.deps/phyml_mpi-bionj.Po rm -f ./.deps/phyml_mpi-cl.Po rm -f ./.deps/phyml_mpi-date.Po rm -f ./.deps/phyml_mpi-draw.Po rm -f ./.deps/phyml_mpi-eigen.Po rm -f ./.deps/phyml_mpi-free.Po rm -f ./.deps/phyml_mpi-help.Po rm -f ./.deps/phyml_mpi-init.Po rm -f ./.deps/phyml_mpi-interface.Po rm -f ./.deps/phyml_mpi-io.Po rm -f ./.deps/phyml_mpi-lk.Po rm -f ./.deps/phyml_mpi-main.Po rm -f ./.deps/phyml_mpi-make.Po rm -f ./.deps/phyml_mpi-mcmc.Po rm -f ./.deps/phyml_mpi-mg.Po rm -f ./.deps/phyml_mpi-mixt.Po rm -f ./.deps/phyml_mpi-models.Po rm -f ./.deps/phyml_mpi-mpi_boot.Po rm -f ./.deps/phyml_mpi-nexus.Po rm -f ./.deps/phyml_mpi-optimiz.Po rm -f ./.deps/phyml_mpi-pars.Po rm -f ./.deps/phyml_mpi-rates.Po rm -f ./.deps/phyml_mpi-simu.Po rm -f ./.deps/phyml_mpi-spr.Po rm -f ./.deps/phyml_mpi-sse.Po rm -f ./.deps/phyml_mpi-stats.Po rm -f ./.deps/phyml_mpi-tbe.Po rm -f ./.deps/phyml_mpi-times.Po rm -f ./.deps/phyml_mpi-tiporder.Po rm -f ./.deps/phyml_mpi-utilities.Po rm -f ./.deps/phyml_mpi-xml.Po rm -f ./.deps/phyrex.Po rm -f ./.deps/rates.Po rm -f ./.deps/rrw.Po rm -f ./.deps/rw.Po rm -f ./.deps/simu.Po rm -f ./.deps/slfv.Po rm -f ./.deps/spr.Po rm -f ./.deps/sse.Po rm -f ./.deps/stats.Po rm -f ./.deps/tbe.Po rm -f ./.deps/times.Po rm -f ./.deps/tiporder.Po rm -f ./.deps/utilities.Po rm -f ./.deps/xml.Po rm -f Makefile make[3]: Leaving directory '/build/phyml-3.3.20200621/src' make[3]: Entering directory '/build/phyml-3.3.20200621' test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/build/phyml-3.3.20200621' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/phyml-3.3.20200621' dh_auto_configure -- --enable-mpi ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-mpi checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking dependency style of gcc... (cached) none configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf" checking for log in -lm... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for mpi-c... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j3 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/phyml-3.3.20200621' make all-recursive make[3]: Entering directory '/build/phyml-3.3.20200621' Making all in src make[4]: Entering directory '/build/phyml-3.3.20200621/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c .: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c In file included from lk.h:18, from lk.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from lk.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c utilities.c: In function 'Assign_State_With_Ambiguity': utilities.c:3073:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 3073 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:3073:26: note: directive argument in the range [0, 2147483647] 3073 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from utilities.c:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c In file included from cl.h:21, from cl.c:13: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/unistd.h:25, from cl.h:19, from cl.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-rates.o `test -f 'rates.c' || echo './'`rates.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-times.o `test -f 'times.c' || echo './'`times.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-tiporder.o `test -f 'tiporder.c' || echo './'`tiporder.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mg.o `test -f 'mg.c' || echo './'`mg.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c io.c: In function 'Print_Fp_Out': io.c:2315:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2315:43: note: directive argument in the range [1, 2147483647] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from io.h:18, from io.c:13: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-date.o `test -f 'date.c' || echo './'`date.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c In file included from sse.h:18, from sse.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from sse.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c In file included from avx.h:18, from avx.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from avx.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c gcc -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm Done. make[4]: Leaving directory '/build/phyml-3.3.20200621/src' make[4]: Entering directory '/build/phyml-3.3.20200621' make[4]: Leaving directory '/build/phyml-3.3.20200621' make[3]: Leaving directory '/build/phyml-3.3.20200621' make[2]: Leaving directory '/build/phyml-3.3.20200621' # move phyml binary to temporary dir inside debian/ # mkdir -p /build/phyml-3.3.20200621/debian/bin mv src/phyml-mpi /build/phyml-3.3.20200621/debian/bin/phyml-mpi mv phyml-manual.pdf doc make[1]: Leaving directory '/build/phyml-3.3.20200621' dh_auto_test make -j3 check VERBOSE=1 make[1]: Entering directory '/build/phyml-3.3.20200621' Making check in src make[2]: Entering directory '/build/phyml-3.3.20200621/src' gcc -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm .: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :. Done. make[2]: Leaving directory '/build/phyml-3.3.20200621/src' make[2]: Entering directory '/build/phyml-3.3.20200621' make[2]: Leaving directory '/build/phyml-3.3.20200621' make[1]: Leaving directory '/build/phyml-3.3.20200621' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/phyml-3.3.20200621' dh_auto_install make -j3 install DESTDIR=/build/phyml-3.3.20200621/debian/phyml AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/phyml-3.3.20200621' Making install in src make[3]: Entering directory '/build/phyml-3.3.20200621/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :. Done. make[4]: Entering directory '/build/phyml-3.3.20200621/src' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/phyml-3.3.20200621/debian/phyml/usr/bin' /usr/bin/install -c phyml-mpi '/build/phyml-3.3.20200621/debian/phyml/usr/bin' make[4]: Leaving directory '/build/phyml-3.3.20200621/src' make[3]: Leaving directory '/build/phyml-3.3.20200621/src' make[3]: Entering directory '/build/phyml-3.3.20200621' make[4]: Entering directory '/build/phyml-3.3.20200621' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/phyml-3.3.20200621' make[3]: Leaving directory '/build/phyml-3.3.20200621' make[2]: Leaving directory '/build/phyml-3.3.20200621' # install phyml binary we have kept safe above mkdir -p /build/phyml-3.3.20200621/debian/phyml/usr/lib/phyml/bin mv /build/phyml-3.3.20200621/debian/bin/* /build/phyml-3.3.20200621/debian/phyml/usr/lib/phyml/bin chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml* make[1]: Leaving directory '/build/phyml-3.3.20200621' dh_install debian/rules override_dh_installdocs make[1]: Entering directory '/build/phyml-3.3.20200621' dh_installdocs mv /build/phyml-3.3.20200621/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /build/phyml-3.3.20200621/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf make[1]: Leaving directory '/build/phyml-3.3.20200621' dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/phyml-3.3.20200621' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/phyml-3.3.20200621' debian/rules override_dh_fixperms make[1]: Entering directory '/build/phyml-3.3.20200621' dh_fixperms find debian/*/usr/share/doc -name "*.nxs" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.xml" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.mat" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.txt" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/phyml-3.3.20200621' dh_missing debian/rules override_dh_dwz make[1]: Entering directory '/build/phyml-3.3.20200621' echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/build/phyml-3.3.20200621' dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phyml' in '../phyml_3.3.20200621-1_armhf.deb'. dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20200621-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phyml_3.3.20200621-1_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: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/14924 and its subdirectories I: Current time: Tue Aug 10 04:56:33 -12 2021 I: pbuilder-time-stamp: 1628614593 Tue Aug 10 16:56:54 UTC 2021 I: 1st build successful. Starting 2nd build on remote node jtx1c-armhf-rb.debian.net. Tue Aug 10 16:56:54 UTC 2021 I: Preparing to do remote build '2' on jtx1c-armhf-rb.debian.net. Tue Aug 10 17:02:48 UTC 2021 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. Tue Aug 10 17:02:52 UTC 2021 I: phyml_3.3.20200621-1_armhf.changes: Format: 1.8 Date: Wed, 22 Jul 2020 16:25:36 +0000 Source: phyml Binary: phyml phyml-dbgsym Architecture: armhf Version: 3:3.3.20200621-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Shayan Doust Description: phyml - Phylogenetic estimation using Maximum Likelihood Closes: 957679 Changes: phyml (3:3.3.20200621-1) unstable; urgency=medium . * Team upload * New upstream version 3.3.20200621 (Closes: #957679) * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Checksums-Sha1: 599ad193a448d7ed438dc9a9a92dcc494db9c232 42548 phyml-dbgsym_3.3.20200621-1_armhf.deb 008573a221c05a31aeee4394a7b4da330282523b 6491 phyml_3.3.20200621-1_armhf.buildinfo 3ce10f210d5a2a15f8dcca24ec82bc43a1a8bce6 1565964 phyml_3.3.20200621-1_armhf.deb Checksums-Sha256: c6d63795c712c2b826a0bd0910b6cb2aff594ef472e36c64ed9b2e5313bbd907 42548 phyml-dbgsym_3.3.20200621-1_armhf.deb 01521f2378fb112050aa1246cd3b57b9fb024804d33798fd781f489897554c2c 6491 phyml_3.3.20200621-1_armhf.buildinfo 19b2103fd066deb79b77d0ac9de38d4baa63d57713e389a8006edcc47c3c6bdb 1565964 phyml_3.3.20200621-1_armhf.deb Files: bbf145d33ee77fa72b8a1c30bfdb7386 42548 debug optional phyml-dbgsym_3.3.20200621-1_armhf.deb f428b64446a12b2f8101163c6d737055 6491 science optional phyml_3.3.20200621-1_armhf.buildinfo 7b7dda45d80cb7fe04788b32e0d12d5b 1565964 science optional phyml_3.3.20200621-1_armhf.deb Tue Aug 10 17:02:53 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.HyyWoYf6g0/phyml_3.3.20200621-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.HyyWoYf6g0/phyml_3.3.20200621-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.HyyWoYf6g0/phyml_3.3.20200621-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.HyyWoYf6g0/b1/phyml_3.3.20200621-1_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.HyyWoYf6g0/b2/phyml_3.3.20200621-1_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: 0.269s) 0.269s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.034s) 0.033s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Aug 10 17:03:17 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Aug 10 17:03:17 UTC 2021 I: phyml from bullseye built successfully and reproducibly on armhf. Tue Aug 10 17:03:18 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Aug 10 17:03:18 UTC 2021 I: Submitting 8.0K b1/phyml_3.3.20200621-1_armhf.buildinfo.asc Tue Aug 10 17:03:20 UTC 2021 I: Submitting 8.0K b2/phyml_3.3.20200621-1_armhf.buildinfo.asc Tue Aug 10 17:03:21 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Aug 10 17:03:21 UTC 2021 I: Done submitting .buildinfo files. Tue Aug 10 17:03:21 UTC 2021 I: Removing signed phyml_3.3.20200621-1_armhf.buildinfo.asc files: removed './b1/phyml_3.3.20200621-1_armhf.buildinfo.asc' removed './b2/phyml_3.3.20200621-1_armhf.buildinfo.asc'