I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 19 00:57:42 +14 2021 I: pbuilder-time-stamp: 1626605862 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 [libpdb-redo_1.0.2-2.dsc] I: copying [./libpdb-redo_1.0.2.orig.tar.gz] I: copying [./libpdb-redo_1.0.2-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.lbs9Jhcc/trustedkeys.kbx': General error gpgv: Signature made Thu Jan 7 00:54:36 2021 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libpdb-redo_1.0.2-2.dsc dpkg-source: info: extracting libpdb-redo in libpdb-redo-1.0.2 dpkg-source: info: unpacking libpdb-redo_1.0.2.orig.tar.gz dpkg-source: info: unpacking libpdb-redo_1.0.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-data-update.patch dpkg-source: info: applying unit-test.patch dpkg-source: info: applying configure.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7603/tmp/hooks/D01_modify_environment starting debug: Running on virt64b. 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/7603/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/7603/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]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.1.4(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,-fixfilepath 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=912dc44b051f4fe49d2b30d92ccb1653 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=7603 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.80Tx2gR5DF/pbuilderrc_HZra --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.80Tx2gR5DF/b2 --logfile b2/build.log --extrapackages usrmerge libpdb-redo_1.0.2-2.dsc' SUDO_GID=113 SUDO_UID=107 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 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash -rwxr-xr-x 1 root root 75880 Sep 23 2020 date -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd -rwxr-xr-x 1 root root 59912 Sep 23 2020 df -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir -rwxr-xr-x 1 root root 55012 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln -rwxr-xr-x 1 root root 35068 Feb 8 2020 login -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 19 00:58 sh -> bash lrwxrwxrwx 1 root root 4 Jul 17 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch -rwxr-xr-x 1 root root 22496 Sep 23 2020 true -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/7603/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), libcifpp-dev (>= 1.0.1), autoconf-archive, libnewuoa-dev, pkg-config, libgsl-dev, libboost-dev, libboost-iostreams-dev, libzeep-dev (>= 5.0.2), libclipper-dev, libccp4-dev (>= 6.5.1-5) 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 libcifpp-dev (>= 1.0.1); however: Package libcifpp-dev is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on libnewuoa-dev; however: Package libnewuoa-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libzeep-dev (>= 5.0.2); however: Package libzeep-dev is not installed. pbuilder-satisfydepends-dummy depends on libclipper-dev; however: Package libclipper-dev is not installed. pbuilder-satisfydepends-dummy depends on libccp4-dev (>= 6.5.1-5); however: Package libccp4-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} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fftw-dev{a} fftw2{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-date-time-dev{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost1.74-dev{a} libbsd0{a} libccp4-data{a} libccp4-dev{a} libccp4c0{a} libccp4f0{a} libcifpp-dev{a} libcifpp1{a} libclipper-dev{a} libclipper2{a} libdebhelper-perl{a} libelf1{a} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgsl-dev{a} libgsl25{a} libgslcblas0{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu-dev{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmmdb2-0{a} libmmdb2-dev{a} libnewuoa-dev{a} libnewuoa0{a} libnl-3-200{a} libnl-route-3-200{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{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} libzeep-dev{a} libzeep5{a} m4{a} man-db{a} ocl-icd-libopencl1{a} pkg-config{a} po-debconf{a} sensible-utils{a} sfftw-dev{a} sfftw2{a} The following packages are RECOMMENDED but will NOT be installed: curl ibverbs-providers libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 55.3 MB of archives. After unpacking 328 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-7 [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 autoconf-archive all 20190106-2.1 [746 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [127 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libnl-3-200 armhf 3.4.0-1+b1 [55.5 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libnl-route-3-200 armhf 3.4.0-1+b1 [136 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libibverbs1 armhf 33.2-1 [53.0 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf librdmacm1 armhf 33.2-1 [60.8 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libfabric1 armhf 1.11.0-2 [319 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libhwloc15 armhf 2.4.1+dfsg-1 [125 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libmd0 armhf 1.0.3-3 [27.4 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libbsd0 armhf 0.11.3-1 [103 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libxcb1 armhf 1.14-3 [136 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libx11-data all 2:1.7.1-1 [310 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf libx11-6 armhf 2:1.7.1-1 [712 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libxnvctrl0 armhf 460.73.01-1 [25.8 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.7 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf libhwloc-plugins armhf 2.4.1+dfsg-1 [19.7 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf libpmix2 armhf 4.0.0-4 [487 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf libopenmpi3 armhf 4.1.0-10 [1831 kB] Get: 55 http://deb.debian.org/debian bullseye/main armhf fftw2 armhf 2.1.5-4.2+b1 [248 kB] Get: 56 http://deb.debian.org/debian bullseye/main armhf fftw-dev armhf 2.1.5-4.2+b1 [268 kB] Get: 57 http://deb.debian.org/debian bullseye/main armhf icu-devtools armhf 67.1-7 [180 kB] Get: 58 http://deb.debian.org/debian bullseye/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB] Get: 59 http://deb.debian.org/debian bullseye/main armhf libboost-date-time1.74.0 armhf 1.74.0-9 [241 kB] Get: 60 http://deb.debian.org/debian bullseye/main armhf libboost-serialization1.74.0 armhf 1.74.0-9 [321 kB] Get: 61 http://deb.debian.org/debian bullseye/main armhf libboost-serialization1.74-dev armhf 1.74.0-9 [394 kB] Get: 62 http://deb.debian.org/debian bullseye/main armhf libboost-date-time1.74-dev armhf 1.74.0-9 [250 kB] Get: 63 http://deb.debian.org/debian bullseye/main armhf libboost-date-time-dev armhf 1.74.0.3 [4332 B] Get: 64 http://deb.debian.org/debian bullseye/main armhf libboost-dev armhf 1.74.0.3 [4548 B] Get: 65 http://deb.debian.org/debian bullseye/main armhf libboost-regex1.74.0 armhf 1.74.0-9 [459 kB] Get: 66 http://deb.debian.org/debian bullseye/main armhf libicu-dev armhf 67.1-7 [9343 kB] Get: 67 http://deb.debian.org/debian bullseye/main armhf libboost-regex1.74-dev armhf 1.74.0-9 [572 kB] Get: 68 http://deb.debian.org/debian bullseye/main armhf libboost-iostreams1.74-dev armhf 1.74.0-9 [271 kB] Get: 69 http://deb.debian.org/debian bullseye/main armhf libboost-iostreams-dev armhf 1.74.0.3 [4316 B] Get: 70 http://deb.debian.org/debian bullseye/main armhf libboost-program-options1.74.0 armhf 1.74.0-9 [339 kB] Get: 71 http://deb.debian.org/debian bullseye/main armhf libboost-program-options1.74-dev armhf 1.74.0-9 [384 kB] Get: 72 http://deb.debian.org/debian bullseye/main armhf libboost-program-options-dev armhf 1.74.0.3 [4340 B] Get: 73 http://deb.debian.org/debian bullseye/main armhf libboost-system1.74.0 armhf 1.74.0-9 [242 kB] Get: 74 http://deb.debian.org/debian bullseye/main armhf libboost-system1.74-dev armhf 1.74.0-9 [243 kB] Get: 75 http://deb.debian.org/debian bullseye/main armhf libboost-system-dev armhf 1.74.0.3 [4468 B] Get: 76 http://deb.debian.org/debian bullseye/main armhf libccp4-data all 6.5.1-5 [61.6 kB] Get: 77 http://deb.debian.org/debian bullseye/main armhf libccp4c0 armhf 6.5.1-5 [75.1 kB] Get: 78 http://deb.debian.org/debian bullseye/main armhf libgfortran5 armhf 10.2.1-6 [237 kB] Get: 79 http://deb.debian.org/debian bullseye/main armhf libmmdb2-0 armhf 2.0.5-1 [272 kB] Get: 80 http://deb.debian.org/debian bullseye/main armhf libccp4f0 armhf 6.5.1-5 [207 kB] Get: 81 http://deb.debian.org/debian bullseye/main armhf libccp4-dev armhf 6.5.1-5 [42.8 kB] Get: 82 http://deb.debian.org/debian bullseye/main armhf libcifpp1 armhf 1.0.1-3 [1335 kB] Get: 83 http://deb.debian.org/debian bullseye/main armhf libcifpp-dev armhf 1.0.1-3 [65.1 kB] Get: 84 http://deb.debian.org/debian bullseye/main armhf sfftw2 armhf 2.1.5-4.2+b1 [236 kB] Get: 85 http://deb.debian.org/debian bullseye/main armhf libclipper2 armhf 2.1.20201109-1 [1095 kB] Get: 86 http://deb.debian.org/debian bullseye/main armhf libmmdb2-dev armhf 2.0.5-1 [91.9 kB] Get: 87 http://deb.debian.org/debian bullseye/main armhf sfftw-dev armhf 2.1.5-4.2+b1 [257 kB] Get: 88 http://deb.debian.org/debian bullseye/main armhf libclipper-dev armhf 2.1.20201109-1 [82.6 kB] Get: 89 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 90 http://deb.debian.org/debian bullseye/main armhf libgslcblas0 armhf 2.6+dfsg-2 [80.0 kB] Get: 91 http://deb.debian.org/debian bullseye/main armhf libgsl25 armhf 2.6+dfsg-2 [769 kB] Get: 92 http://deb.debian.org/debian bullseye/main armhf libgsl-dev armhf 2.6+dfsg-2 [963 kB] Get: 93 http://deb.debian.org/debian bullseye/main armhf libnewuoa0 armhf 0.1.1-2 [15.4 kB] Get: 94 http://deb.debian.org/debian bullseye/main armhf libnewuoa-dev armhf 0.1.1-2 [4916 B] Get: 95 http://deb.debian.org/debian bullseye/main armhf libzeep5 armhf 5.0.2-3 [577 kB] Get: 96 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Get: 97 http://deb.debian.org/debian bullseye/main armhf libzeep-dev armhf 5.0.2-3 [1092 kB] Fetched 55.3 MB in 12s (4656 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_armhf.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... 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Unpacking libboost-date-time1.74-dev:armhf (1.74.0-9) ... Selecting previously unselected package libboost-date-time-dev:armhf. Preparing to unpack .../62-libboost-date-time-dev_1.74.0.3_armhf.deb ... Unpacking libboost-date-time-dev:armhf (1.74.0.3) ... Selecting previously unselected package libboost-dev:armhf. Preparing to unpack .../63-libboost-dev_1.74.0.3_armhf.deb ... Unpacking libboost-dev:armhf (1.74.0.3) ... Selecting previously unselected package libboost-regex1.74.0:armhf. Preparing to unpack .../64-libboost-regex1.74.0_1.74.0-9_armhf.deb ... Unpacking libboost-regex1.74.0:armhf (1.74.0-9) ... Selecting previously unselected package libicu-dev:armhf. Preparing to unpack .../65-libicu-dev_67.1-7_armhf.deb ... Unpacking libicu-dev:armhf (67.1-7) ... Selecting previously unselected package libboost-regex1.74-dev:armhf. Preparing to unpack .../66-libboost-regex1.74-dev_1.74.0-9_armhf.deb ... Unpacking libboost-regex1.74-dev:armhf (1.74.0-9) ... Selecting previously unselected package libboost-iostreams1.74-dev:armhf. Preparing to unpack .../67-libboost-iostreams1.74-dev_1.74.0-9_armhf.deb ... Unpacking libboost-iostreams1.74-dev:armhf (1.74.0-9) ... Selecting previously unselected package libboost-iostreams-dev:armhf. Preparing to unpack .../68-libboost-iostreams-dev_1.74.0.3_armhf.deb ... Unpacking libboost-iostreams-dev:armhf (1.74.0.3) ... Selecting previously unselected package libboost-program-options1.74.0:armhf. Preparing to unpack .../69-libboost-program-options1.74.0_1.74.0-9_armhf.deb ... Unpacking libboost-program-options1.74.0:armhf (1.74.0-9) ... Selecting previously unselected package libboost-program-options1.74-dev:armhf. Preparing to unpack .../70-libboost-program-options1.74-dev_1.74.0-9_armhf.deb ... Unpacking libboost-program-options1.74-dev:armhf (1.74.0-9) ... Selecting previously unselected package libboost-program-options-dev:armhf. 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Unpacking libccp4c0:armhf (6.5.1-5) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../77-libgfortran5_10.2.1-6_armhf.deb ... Unpacking libgfortran5:armhf (10.2.1-6) ... Selecting previously unselected package libmmdb2-0:armhf. Preparing to unpack .../78-libmmdb2-0_2.0.5-1_armhf.deb ... Unpacking libmmdb2-0:armhf (2.0.5-1) ... Selecting previously unselected package libccp4f0:armhf. Preparing to unpack .../79-libccp4f0_6.5.1-5_armhf.deb ... Unpacking libccp4f0:armhf (6.5.1-5) ... Selecting previously unselected package libccp4-dev:armhf. Preparing to unpack .../80-libccp4-dev_6.5.1-5_armhf.deb ... Unpacking libccp4-dev:armhf (6.5.1-5) ... Selecting previously unselected package libcifpp1. Preparing to unpack .../81-libcifpp1_1.0.1-3_armhf.deb ... Unpacking libcifpp1 (1.0.1-3) ... Selecting previously unselected package libcifpp-dev. Preparing to unpack .../82-libcifpp-dev_1.0.1-3_armhf.deb ... Unpacking libcifpp-dev (1.0.1-3) ... 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Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:armhf (460.73.01-1) ... Setting up libboost-iostreams1.74-dev:armhf (1.74.0-9) ... Setting up dh-autoreconf (20) ... Setting up libboost-date-time1.74-dev:armhf (1.74.0-9) ... Setting up libboost-date-time-dev:armhf (1.74.0.3) ... Setting up librdmacm1:armhf (33.2-1) ... Setting up debhelper (13.3.4) ... Setting up libboost-iostreams-dev:armhf (1.74.0.3) ... Setting up libhwloc-plugins:armhf (2.4.1+dfsg-1) ... Setting up libzeep-dev (5.0.2-3) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:armhf (4.0.0-4) ... Setting up libopenmpi3:armhf (4.1.0-10) ... Setting up sfftw2 (2.1.5-4.2+b1) ... Setting up fftw2 (2.1.5-4.2+b1) ... Setting up sfftw-dev (2.1.5-4.2+b1) ... Setting up libclipper2:armhf (2.1.20201109-1) ... Setting up fftw-dev (2.1.5-4.2+b1) ... Setting up libclipper-dev:armhf (2.1.20201109-1) ... Processing triggers for libc-bin (2.31-12) ... 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... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (390 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 39745 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... 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I: Building the package hostname: Name or service not known I: Running cd /build/libpdb-redo-1.0.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libpdb-redo_1.0.2-2_source.changes dpkg-buildpackage: info: source package libpdb-redo dpkg-buildpackage: info: source version 1.0.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Maarten L. Hekkelman dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. debian/rules override_dh_auto_configure make[1]: ingresso nella directory «/build/libpdb-redo-1.0.2» dh_auto_configure -- --enable-shared --disable-static ./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-shared --disable-static checking for g++... g++ 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 g++ accepts -g... yes checking whether g++ supports C++17 features with -std=c++17... yes checking for a BSD-compatible install... /usr/bin/install -c checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking how to print strings... printf checking for gcc... gcc 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 for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... no checking for mawk... mawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -std=c++17 -E checking for ld used by g++ -std=c++17... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ -std=c++17 linker (/usr/bin/ld) supports shared libraries... yes checking for g++ -std=c++17 option to produce PIC... -fPIC -DPIC checking if g++ -std=c++17 PIC flag -fPIC -DPIC works... yes checking if g++ -std=c++17 static flag -static works... yes checking if g++ -std=c++17 supports -c -o file.o... yes checking if g++ -std=c++17 supports -c -o file.o... (cached) yes checking whether the g++ -std=c++17 linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C++ compiler accepts -fstandalone-debug... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for mrc... USE_RSRC=1 checking for sin in -lm... yes checking for gsl ... yes checking whether gcc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for boostlib >= 1.71 (107100)... yes checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes checking filesystem usability... yes checking filesystem presence... yes checking for filesystem... yes checking endian.h usability... yes checking endian.h presence... yes checking for endian.h... yes checking for libcifpp ... yes checking for libzeep ... yes checking for clipper ... yes checking clipper version... ok checking dlib/global_optimization.h usability... no checking dlib/global_optimization.h presence... no checking for dlib/global_optimization.h... no configure: WARNING: libdlib-dev not found checking for newuoa ... yes configure: creating ./config.status config.status: creating GNUmakefile config.status: creating libpdb-redo.pc config.status: creating src/config.hpp config.status: executing libtool commands make[1]: uscita dalla directory «/build/libpdb-redo-1.0.2» dh_auto_build make -j4 make[1]: ingresso nella directory «/build/libpdb-redo-1.0.2» mkdir -p obj >> src/AtomShape.cpp >> src/BondMap.cpp >> src/ClipperWrapper.cpp >> src/DistanceMap.cpp >> src/MapMaker.cpp >> src/Minimizer.cpp In file included from /usr/include/c++/10/vector:72, from /usr/include/cif++/CifUtils.hpp:31, from src/DistanceMap.cpp:32: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> src/Ramachandran.cpp In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/algorithm:62, from src/BondMap.cpp:30: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mmcif::{anonymous}::CompoundBondInfo; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/algorithm:62, from src/BondMap.cpp:30: /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]’: /usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]’: /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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_comp_iter >]’: /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ >> src/ResolutionCalculator.cpp /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/MapMaker.cpp: In member function ‘void mmcif::MapMaker::fixMTZ() [with FTYPE = float]’: src/MapMaker.cpp:1033:8: note: parameter passing for argument of type ‘clipper::datatypes::F_phi’ when C++17 is enabled changed to match C++14 in GCC 10.1 1033 | auto mFo = mFbData[ih] - mFdData[ih]; | ^~~ /usr/include/c++/10/bits/stl_algo.h: In function ‘void mmcif::createBondInfoFile(const std::filesystem::__cxx11::path&, const std::filesystem::__cxx11::path&)’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ >> src/Restraints.cpp In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/functional:62, from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/10/algorithm:74, from /usr/include/c++/10/regex:38, from src/Minimizer.cpp:35: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {TransPeptideRestraint}; _Tp = TransPeptideRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PlanarityRestraint}; _Tp = PlanarityRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PlanarityRestraint}; _Tp = PlanarityRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, float&, float&}; _Tp = BondRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, unsigned int, float&, float&}; _Tp = BondRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, float&, float&}; _Tp = AngleRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, float&, float&}; _Tp = AngleRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, unsigned int, float}; _Tp = ChiralVolumeRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {unsigned int&, unsigned int&, double&, double}; _Tp = NonBondedContactRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {unsigned int, unsigned int, unsigned int, unsigned int, float&}; _Tp = ChiralVolumeRestraint; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘void Minimizer::addLinkRestraints(const mmcif::Monomer&, const mmcif::Monomer&, const mmcif::Link&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ >> src/SkipList.cpp In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/functional:62, from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/10/algorithm:74, from /usr/include/c++/10/ext/slist:47, from /usr/include/boost/algorithm/string/std/slist_traits.hpp:16, from /usr/include/boost/algorithm/string/std_containers_traits.hpp:23, from /usr/include/boost/algorithm/string.hpp:18, from src/Restraints.cpp:36: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/c++/10/functional:62, from /usr/include/c++/10/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/10/algorithm:74, from /usr/include/c++/10/ext/slist:47, from /usr/include/boost/algorithm/string/std/slist_traits.hpp:16, from /usr/include/boost/algorithm/string/std_containers_traits.hpp:23, from /usr/include/boost/algorithm/string.hpp:18, from src/Restraints.cpp:36: /usr/include/c++/10/bits/stl_vector.h: In member function ‘std::vector clipper::Matrix::eigen(bool) [with T = double]’: /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/boost/format.hpp:17, from src/MapMaker.cpp:33: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:67, from /usr/include/boost/format.hpp:17, from src/MapMaker.cpp:33: /usr/include/c++/10/bits/stl_vector.h: In constructor ‘clipper::BasisFn_spline::BasisFn_spline(const clipper::HKL_data_base&, const int&, clipper::ftype)’: /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/boost/format.hpp:17, from src/MapMaker.cpp:33: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {clipper::Atom}; _Tp = clipper::Atom; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::Atom}; _Tp = clipper::Atom; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> src/Statistics.cpp /usr/include/c++/10/bits/vector.tcc: In constructor ‘Minimizer::Minimizer(const mmcif::Polymer&, int, int, const mmcif::BondMap&, const XMap&, float, float)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/istream:38, from /usr/include/c++/10/fstream:38, from src/Statistics.cpp:29: /usr/include/c++/10/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double; _T2 = double; typename std::__strip_reference_wrapper::type>::__type = double; typename std::__strip_reference_wrapper::type>::__type = double]’: src/Statistics.cpp:610:80: required from here /usr/include/c++/10/bits/stl_pair.h:567:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 567 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ >> src/Symmetry-2.cpp In file included from /usr/include/c++/10/bits/stl_algo.h:61, from /usr/include/c++/10/functional:65, from /usr/include/cif++/Point.hpp:29, from /usr/include/cif++/Structure.hpp:32, from src/Statistics.cpp:32: /usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/10/functional:65, from /usr/include/cif++/Point.hpp:29, from /usr/include/cif++/Structure.hpp:32, from src/Statistics.cpp:32: /usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/functional:62, from /usr/include/cif++/Point.hpp:29, from /usr/include/cif++/Structure.hpp:32, from src/Statistics.cpp:32: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mmcif::ResidueStatistics}; _Tp = mmcif::ResidueStatistics; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const clipper::Coord_grid&, double&}; _Tp = mmcif::AtomGridData; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘void mmcif::StatsCollector::sumDensity(std::vector&, mmcif::StatsCollector::GridPtDataMap&, std::map, std::vector >&) const’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mmcif::Atom&, float&}; _Tp = mmcif::AtomData; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {mmcif::Atom&, float&}; _Tp = mmcif::AtomData; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/functional:65, from /usr/include/cif++/Point.hpp:29, from /usr/include/cif++/Structure.hpp:32, from src/Statistics.cpp:32: /usr/include/c++/10/bits/stl_algo.h: In member function ‘void mmcif::StatsCollector::initialize()’: /usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/functional:62, from /usr/include/cif++/Point.hpp:29, from /usr/include/cif++/Structure.hpp:32, from src/Statistics.cpp:32: /usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector mmcif::StatsCollector::collect(const std::vector, std::allocator >, int, std::__cxx11::basic_string, std::allocator >, std::__cxx11::basic_string, std::allocator > > >&, mmcif::BoundingBox&, bool) const’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/cif++/CifUtils.hpp:31, from src/Symmetry-2.cpp:33: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {clipper::Coord_orth}; _Tp = clipper::Coord_orth; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In function ‘clipper::Coord_orth CalculateOffsetForCell(const mmcif::Structure&, const clipper::Spacegroup&, const clipper::Cell&)’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {clipper::RTop_orth}; _Tp = clipper::RTop_orth; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh /build/libpdb-redo-1.0.2/libtool --silent --tag=CXX --mode=link g++ -std=c++17 -g -O2 -fdebug-prefix-map=/build/libpdb-redo-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wall -Wno-multichar -I include -O2 -DDATADIR='"/usr/share/libpdb-redo"' -DNDEBUG -Wl,-z,relro -Wl,-z,now -pthread -version-info 1:0:0 -o libpdb-redo.la -rpath /usr/lib/arm-linux-gnueabihf obj/AtomShape.lo obj/BondMap.lo obj/ClipperWrapper.lo obj/DistanceMap.lo obj/MapMaker.lo obj/Minimizer.lo obj/Ramachandran.lo obj/ResolutionCalculator.lo obj/Restraints.lo obj/SkipList.lo obj/Statistics.lo obj/Symmetry-2.lo -lcifpp -lzeep -lgsl -lgslcblas -lm -lnewuoa -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lboost_iostreams -lm make[1]: uscita dalla directory «/build/libpdb-redo-1.0.2» debian/rules override_dh_auto_test make[1]: ingresso nella directory «/build/libpdb-redo-1.0.2» make test make[2]: ingresso nella directory «/build/libpdb-redo-1.0.2» >> test/unit-test.cpp In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/functional:62, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:37, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/test/execution_monitor.hpp:24, from /usr/include/boost/test/impl/compiler_log_formatter.ipp:22, from /usr/include/boost/test/included/unit_test.hpp:18, from test/unit-test.cpp:28: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {TestResidue}; _Tp = TestResidue; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/vector.tcc: In member function ‘void stats_1::test_method()’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> building unit-test g++ -std=c++17 -g -O2 -fdebug-prefix-map=/build/libpdb-redo-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wall -Wno-multichar -I include -O2 -DDATADIR='"/usr/share/libpdb-redo"' -DNDEBUG -Wl,-z,relro -Wl,-z,now -pthread -o test/unit-test obj/unit-test.o -L.libs -lpdb-redo -lcifpp -lzeep -lgsl -lgslcblas -lm -lnewuoa -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lboost_iostreams -lm cd test; BOND_INFO_FILE=/build/libpdb-redo-1.0.2/rsrc/bond-info.bin.gz LD_LIBRARY_PATH=../.libs ./unit-test Running 7 test cases... Missing bond information for compound U_K Missing information for compound 'U_K' Missing bond information for compound U_K *** No errors detected make[2]: uscita dalla directory «/build/libpdb-redo-1.0.2» make[1]: uscita dalla directory «/build/libpdb-redo-1.0.2» create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/libpdb-redo-1.0.2/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: ingresso nella directory «/build/libpdb-redo-1.0.2» install -d /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/arm-linux-gnueabihf /bin/sh /build/libpdb-redo-1.0.2/libtool --mode=install install libpdb-redo.la /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/arm-linux-gnueabihf libtool: install: install .libs/libpdb-redo.so.1.0.0 /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/arm-linux-gnueabihf/libpdb-redo.so.1.0.0 libtool: install: (cd /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libpdb-redo.so.1.0.0 libpdb-redo.so.1 || { rm -f libpdb-redo.so.1 && ln -s libpdb-redo.so.1.0.0 libpdb-redo.so.1; }; }) libtool: install: (cd /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/arm-linux-gnueabihf && { ln -s -f libpdb-redo.so.1.0.0 libpdb-redo.so || { rm -f libpdb-redo.so && ln -s libpdb-redo.so.1.0.0 libpdb-redo.so; }; }) libtool: install: install .libs/libpdb-redo.lai /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/arm-linux-gnueabihf/libpdb-redo.la libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' install -d /build/libpdb-redo-1.0.2/debian/tmp/usr/include/pdb-redo for f in AtomShape.hpp BondMap.hpp ClipperWrapper.hpp DistanceMap.hpp MapMaker.hpp Minimizer.hpp Ramachandran.hpp ResolutionCalculator.hpp Restraints.hpp SkipList.hpp Statistics.hpp Symmetry-2.hpp; do install include/pdb-redo/$f /build/libpdb-redo-1.0.2/debian/tmp/usr/include/pdb-redo/$f; done install -d /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig install -m 644 libpdb-redo.pc /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/libpdb-redo.pc install -d /build/libpdb-redo-1.0.2/debian/tmp/usr/share/libpdb-redo install -m 644 rsrc/bond-info.bin.gz /build/libpdb-redo-1.0.2/debian/tmp/usr/share/libpdb-redo/bond-info.bin make[1]: uscita dalla directory «/build/libpdb-redo-1.0.2» dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libpdb-redo1/usr/lib/arm-linux-gnueabihf/libpdb-redo.so.1.0.0 found in none of the libraries dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: generazione del pacchetto "libpdb-redo1-dbgsym" in "../libpdb-redo1-dbgsym_1.0.2-2_armhf.deb". dpkg-deb: generazione del pacchetto "libpdb-redo1" in "../libpdb-redo1_1.0.2-2_armhf.deb". dpkg-deb: generazione del pacchetto "libpdb-redo-dev" in "../libpdb-redo-dev_1.0.2-2_armhf.deb". dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libpdb-redo_1.0.2-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/7603/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/7603/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/7603 and its subdirectories I: Current time: Mon Jul 19 01:06:31 +14 2021 I: pbuilder-time-stamp: 1626606391