I: pbuilder: network access will be disabled during build I: Current time: Tue May 19 23:51:57 +14 2020 I: pbuilder-time-stamp: 1589881917 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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 [physamp_1.1.0-1.dsc] I: copying [./physamp_1.1.0.orig.tar.gz] I: copying [./physamp_1.1.0-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Apr 19 09:31:01 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./physamp_1.1.0-1.dsc dpkg-source: info: extracting physamp in physamp-1.1.0 dpkg-source: info: unpacking physamp_1.1.0.orig.tar.gz dpkg-source: info: unpacking physamp_1.1.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying unforce-cxxflags.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/17057/tmp/hooks/D01_modify_environment starting debug: Running on ff2b. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/17057/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/17057/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=c79661669c424d1596c5b650d64f61ed LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=17057 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.js1fLs65lu/pbuilderrc_6gcy --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.js1fLs65lu/b2 --logfile b2/build.log physamp_1.1.0-1.dsc' SUDO_GID=114 SUDO_UID=109 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 4.19.0-9-armmp-lpae #1 SMP Debian 4.19.118-2 (2020-04-29) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash -rwxr-xr-x 1 root root 71648 Mar 1 2019 date -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd -rwxr-xr-x 1 root root 55672 Mar 1 2019 df -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 18260 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln -rwxr-xr-x 1 root root 34932 Jul 27 2018 login -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 10 2019 more -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 May 19 23:53 sh -> bash lrwxrwxrwx 1 root root 4 May 18 22:24 sh.distrib -> dash -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty -rwsr-xr-x 1 root root 42472 Jan 10 2019 su -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch -rwxr-xr-x 1 root root 18260 Mar 1 2019 true -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/17057/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 (>= 11~), cmake, texinfo, libbpp-phyl-dev (>= 2.4.0) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on texinfo; however: Package texinfo is not installed. pbuilder-satisfydepends-dummy depends on libbpp-phyl-dev (>= 2.4.0); however: Package libbpp-phyl-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} bsdmainutils{a} cmake{a} cmake-data{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-seq12{a} libbsd0{a} libcroco3{a} libcurl4{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libicu63{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps7{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtext-unidecode-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml2{a} lsb-base{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} tex-common{a} texinfo{a} ucf{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules libwww-perl libxml-sax-expat-perl lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 35.7 MB of archives. After unpacking 155 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 9 http://deb.debian.org/debian buster/main armhf tex-common all 6.11 [53.1 kB] Get: 10 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libprocps7 armhf 2:3.3.15-2 [58.7 kB] Get: 12 http://deb.debian.org/debian buster/main armhf lsb-base all 10.2019051400 [28.4 kB] Get: 13 http://deb.debian.org/debian buster/main armhf procps armhf 2:3.3.15-2 [248 kB] Get: 14 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 16 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 17 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 19 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 20 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 21 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 22 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 23 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 24 http://deb.debian.org/debian buster/main armhf cmake-data all 3.13.4-1 [1476 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libarchive13 armhf 3.3.3-4+deb10u1 [277 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 40 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libcurl4 armhf 7.64.0-4+deb10u1 [297 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libjsoncpp1 armhf 1.7.4-3 [67.8 kB] Get: 45 http://deb.debian.org/debian buster/main armhf librhash0 armhf 1.3.8-1 [134 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libuv1 armhf 1.24.1-1 [98.0 kB] Get: 47 http://deb.debian.org/debian buster/main armhf cmake armhf 3.13.4-1 [2848 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 49 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 52 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 54 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 56 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 57 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 58 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 59 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 60 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 61 http://deb.debian.org/debian buster/main armhf libbpp-core4 armhf 2.4.1-3 [510 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libbpp-core-dev armhf 2.4.1-3 [951 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libbpp-seq12 armhf 2.4.1-3 [439 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libbpp-phyl12 armhf 2.4.1-2 [1367 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libbpp-seq-dev armhf 2.4.1-3 [753 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libbpp-phyl-dev armhf 2.4.1-2 [3087 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libtext-unidecode-perl all 1.30-1 [103 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libxml-sax-base-perl all 1.09-1 [20.4 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get: 71 http://deb.debian.org/debian buster/main armhf libxml-libxml-perl armhf 2.0134+dfsg-1 [326 kB] Get: 72 http://deb.debian.org/debian buster/main armhf texinfo armhf 6.5.0.dfsg.1-4+b1 [1421 kB] Fetched 35.7 MB in 23s (1558 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0: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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package ucf. Preparing to unpack .../07-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package tex-common. Preparing to unpack .../08-tex-common_6.11_all.deb ... Unpacking tex-common (6.11) ... 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Selecting previously unselected package libbpp-seq12:armhf. Preparing to unpack .../62-libbpp-seq12_2.4.1-3_armhf.deb ... Unpacking libbpp-seq12:armhf (2.4.1-3) ... Selecting previously unselected package libbpp-phyl12:armhf. Preparing to unpack .../63-libbpp-phyl12_2.4.1-2_armhf.deb ... Unpacking libbpp-phyl12:armhf (2.4.1-2) ... Selecting previously unselected package libbpp-seq-dev. Preparing to unpack .../64-libbpp-seq-dev_2.4.1-3_armhf.deb ... Unpacking libbpp-seq-dev (2.4.1-3) ... Selecting previously unselected package libbpp-phyl-dev:armhf. Preparing to unpack .../65-libbpp-phyl-dev_2.4.1-2_armhf.deb ... Unpacking libbpp-phyl-dev:armhf (2.4.1-2) ... Selecting previously unselected package libtext-unidecode-perl. Preparing to unpack .../66-libtext-unidecode-perl_1.30-1_all.deb ... Unpacking libtext-unidecode-perl (1.30-1) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../67-libxml-namespacesupport-perl_1.12-1_all.deb ... 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Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libprocps7:armhf (2:3.3.15-2) ... Setting up libnghttp2-14:armhf (1.36.0-2+deb10u1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libkrb5support0:armhf (1.17-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:armhf (1.24.1-1) ... Setting up libbpp-core4:armhf (2.4.1-3) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up sensible-utils (0.0.12) ... Setting up librhash0:armhf (1.3.8-1) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libssh2-1:armhf (1.8.0-2.1) ... Setting up cmake-data (3.13.4-1) ... Setting up libkrb5-3:armhf (1.17-3) ... Setting up libtext-unidecode-perl (1.30-1) ... Setting up libbpp-seq12:armhf (2.4.1-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libjsoncpp1:armhf (1.7.4-3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libbpp-phyl12:armhf (2.4.1-2) ... Setting up libtool (2.4.6-9) ... Setting up libarchive13:armhf (3.3.3-4+deb10u1) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up libbpp-core-dev (2.4.1-3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libcurl4:armhf (7.64.0-4+deb10u1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libbpp-seq-dev (2.4.1-3) ... Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up intltool-debian (0.35.0+20060710.5) ... Setting up tex-common (6.11) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libbpp-phyl-dev:armhf (2.4.1-2) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up cmake (3.13.4-1) ... Setting up po-debconf (1.0.21) ... Setting up texinfo (6.5.0.dfsg.1-4+b1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.1.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/physamp-1.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package physamp dpkg-buildpackage: info: source version 1.1.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Julien Dutheil dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/physamp-1.1.0' dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo 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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DCMAKE_BUILD_TYPE=RelWithDebInfo .. -- The CXX compiler identification is GNU 8.3.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found /bin/gzip compression program, using file extension .gz -- 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-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 -- Found makeinfo as '/usr/bin/makeinfo': 'info' and 'html' target enabled (builds info/html doc) -- Found texi2dvi: 'pdf' target enabled (builds pdf doc) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/physamp-1.1.0/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/physamp-1.1.0' dh_auto_build cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/physamp-1.1.0 -B/build/physamp-1.1.0/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/physamp-1.1.0/obj-arm-linux-gnueabihf/CMakeFiles /build/physamp-1.1.0/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make -f physamp/CMakeFiles/bppphysamp.dir/build.make physamp/CMakeFiles/bppphysamp.dir/depend make -f physamp/CMakeFiles/bppalnoptim.dir/build.make physamp/CMakeFiles/bppalnoptim.dir/depend make -f docs/CMakeFiles/info.dir/build.make docs/CMakeFiles/info.dir/depend make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/depend make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/physamp-1.1.0 /build/physamp-1.1.0/physamp /build/physamp-1.1.0/obj-arm-linux-gnueabihf /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp/CMakeFiles/bppphysamp.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/physamp-1.1.0 /build/physamp-1.1.0/physamp /build/physamp-1.1.0/obj-arm-linux-gnueabihf /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp/CMakeFiles/bppalnoptim.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/physamp-1.1.0 /build/physamp-1.1.0/man /build/physamp-1.1.0/obj-arm-linux-gnueabihf /build/physamp-1.1.0/obj-arm-linux-gnueabihf/man /build/physamp-1.1.0/obj-arm-linux-gnueabihf/man/CMakeFiles/man.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/physamp-1.1.0 /build/physamp-1.1.0/docs /build/physamp-1.1.0/obj-arm-linux-gnueabihf /build/physamp-1.1.0/obj-arm-linux-gnueabihf/docs /build/physamp-1.1.0/obj-arm-linux-gnueabihf/docs/CMakeFiles/info.dir/DependInfo.cmake --color= Scanning dependencies of target info Scanning dependencies of target man Scanning dependencies of target bppalnoptim make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make -f docs/CMakeFiles/info.dir/build.make docs/CMakeFiles/info.dir/build make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/build make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make -f physamp/CMakeFiles/bppalnoptim.dir/build.make physamp/CMakeFiles/bppalnoptim.dir/build make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' Scanning dependencies of target bppphysamp [ 12%] Generating info page make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make -f physamp/CMakeFiles/bppphysamp.dir/build.make physamp/CMakeFiles/bppphysamp.dir/build cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf/docs && /usr/bin/makeinfo --no-split -o /build/physamp-1.1.0/obj-arm-linux-gnueabihf/docs/physamp.info /build/physamp-1.1.0/docs/physamp.texi [ 25%] Building CXX object physamp/CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/physamp-1.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIE -o CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o -c /build/physamp-1.1.0/physamp/AlignmentOptimizer.cpp [ 37%] Compressing manpage bppalnoptim.1 cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf/man && /bin/gzip -c9n /build/physamp-1.1.0/man/bppalnoptim.1 > /build/physamp-1.1.0/obj-arm-linux-gnueabihf/man/bppalnoptim.1.gz [ 50%] Building CXX object physamp/CMakeFiles/bppphysamp.dir/PhyloSampler.cpp.o cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp && /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/physamp-1.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIE -o CMakeFiles/bppphysamp.dir/PhyloSampler.cpp.o -c /build/physamp-1.1.0/physamp/PhyloSampler.cpp [ 62%] Compressing manpage bppphysamp.1 cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf/man && /bin/gzip -c9n /build/physamp-1.1.0/man/bppphysamp.1 > /build/physamp-1.1.0/obj-arm-linux-gnueabihf/man/bppphysamp.1.gz make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' [ 62%] Built target man [ 75%] Compressing info page cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf/docs && /bin/gzip -c9n /build/physamp-1.1.0/obj-arm-linux-gnueabihf/docs/physamp.info > /build/physamp-1.1.0/obj-arm-linux-gnueabihf/docs/physamp.info.gz make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' [ 75%] Built target info In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Io/FileTools.h:46, from /usr/include/Bpp/App/ApplicationTools.h:44, from /build/physamp-1.1.0/physamp/PhyloSampler.cpp:31: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Index}; _Tp = Index; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/Bpp/Numeric/VectorTools.h:54, from /usr/include/Bpp/Numeric/DataTable.h:43, from /build/physamp-1.1.0/physamp/PhyloSampler.cpp:34: /usr/include/c++/8/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred]': /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function '_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred]': /usr/include/c++/8/bits/stl_algo.h:860:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __remove_if(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:860:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return __find_if(__first, __last, __pred, ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from /usr/include/Bpp/Numeric/VectorTools.h:54, from /usr/include/Bpp/Numeric/DataTable.h:43, from /build/physamp-1.1.0/physamp/PhyloSampler.cpp:34: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Index; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/Bpp/Numeric/VectorTools.h:54, from /usr/include/Bpp/Numeric/DataTable.h:43, from /build/physamp-1.1.0/physamp/PhyloSampler.cpp:34: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from /usr/include/Bpp/Io/FileTools.h:46, from /usr/include/Bpp/App/ApplicationTools.h:44, from /build/physamp-1.1.0/physamp/PhyloSampler.cpp:31: /usr/include/c++/8/bits/vector.tcc: In function 'int main(int, char**)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from /usr/include/Bpp/Numeric/VectorTools.h:54, from /usr/include/Bpp/Numeric/DataTable.h:43, from /build/physamp-1.1.0/physamp/PhyloSampler.cpp:34: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:939:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__remove_if(__first, __last, ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__pred_iter(__pred)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:939:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__remove_if(__first, __last, ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__pred_iter(__pred)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Linking CXX executable bppphysamp cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppphysamp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/physamp-1.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppphysamp.dir/PhyloSampler.cpp.o -o bppphysamp /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 make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' [ 87%] Built target bppphysamp [100%] Linking CXX executable bppalnoptim cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp && /usr/bin/cmake -E cmake_link_script CMakeFiles/bppalnoptim.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/physamp-1.1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bppalnoptim.dir/AlignmentOptimizer.cpp.o -o bppalnoptim /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 make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' [100%] Built target bppalnoptim make[2]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/physamp-1.1.0/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/physamp-1.1.0/debian/physamp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/physamp-1.1.0 -B/build/physamp-1.1.0/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/physamp-1.1.0/obj-arm-linux-gnueabihf/CMakeFiles /build/physamp-1.1.0/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make -f physamp/CMakeFiles/bppphysamp.dir/build.make physamp/CMakeFiles/bppphysamp.dir/depend make -f physamp/CMakeFiles/bppalnoptim.dir/build.make physamp/CMakeFiles/bppalnoptim.dir/depend make -f docs/CMakeFiles/info.dir/build.make docs/CMakeFiles/info.dir/depend make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/depend make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/physamp-1.1.0 /build/physamp-1.1.0/physamp /build/physamp-1.1.0/obj-arm-linux-gnueabihf /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp/CMakeFiles/bppphysamp.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/physamp-1.1.0 /build/physamp-1.1.0/physamp /build/physamp-1.1.0/obj-arm-linux-gnueabihf /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp /build/physamp-1.1.0/obj-arm-linux-gnueabihf/physamp/CMakeFiles/bppalnoptim.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' cd /build/physamp-1.1.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/physamp-1.1.0 /build/physamp-1.1.0/man /build/physamp-1.1.0/obj-arm-linux-gnueabihf 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docs/CMakeFiles/info.dir/build.make docs/CMakeFiles/info.dir/build make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/build make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'physamp/CMakeFiles/bppalnoptim.dir/build'. make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'docs/CMakeFiles/info.dir/build'. make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'physamp/CMakeFiles/bppphysamp.dir/build'. make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'man/CMakeFiles/man.dir/build'. make[3]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' [ 25%] Built target bppalnoptim [ 50%] Built target info [ 75%] Built target bppphysamp [100%] Built target man make[2]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/physamp-1.1.0/obj-arm-linux-gnueabihf/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "RelWithDebInfo" -- Installing: /build/physamp-1.1.0/debian/physamp/usr/bin/bppalnoptim -- Installing: /build/physamp-1.1.0/debian/physamp/usr/bin/bppphysamp -- Installing: /build/physamp-1.1.0/debian/physamp/usr/share/info/physamp.info.gz -- Installing: /build/physamp-1.1.0/debian/physamp/usr/share/man/man1/bppalnoptim.1.gz -- Installing: /build/physamp-1.1.0/debian/physamp/usr/share/man/man1/bppphysamp.1.gz make[1]: Leaving directory '/build/physamp-1.1.0/obj-arm-linux-gnueabihf' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/physamp/usr/bin/bppphysamp contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/physamp/usr/bin/bppalnoptim contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'physamp-dbgsym' in '../physamp-dbgsym_1.1.0-1_armhf.deb'. dpkg-deb: building package 'physamp' in '../physamp_1.1.0-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../physamp_1.1.0-1_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) I: copying local configuration I: user script /srv/workspace/pbuilder/17057/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/17057/tmp/hooks/B01_cleanup finished 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/17057 and its subdirectories I: Current time: Tue May 19 23:57:01 +14 2020 I: pbuilder-time-stamp: 1589882221