I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 4 01:48:06 +14 2023 I: pbuilder-time-stamp: 1685792886 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gemmi_0.5.7+ds-2.dsc] I: copying [./gemmi_0.5.7+ds.orig.tar.xz] I: copying [./gemmi_0.5.7+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Oct 4 22:32:52 2022 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gemmi_0.5.7+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting gemmi in gemmi-0.5.7+ds dpkg-source: info: unpacking gemmi_0.5.7+ds.orig.tar.xz dpkg-source: info: unpacking gemmi_0.5.7+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-tao-pegtl.patch dpkg-source: info: applying use-system-doctest.patch dpkg-source: info: applying tao-pegtl-3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25145/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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 4 01:48 /bin/sh -> /bin/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/25145/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/25145/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.15(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=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=6e2f4c04347e4dbb9365b585cd24e55d 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=25145 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/r-b-build.2hMiqwe5/pbuilderrc_g4uI --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2hMiqwe5/b2 --logfile b2/build.log --extrapackages usrmerge gemmi_0.5.7+ds-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://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash -rwxr-xr-x 1 root root 133220 Sep 21 2022 date -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd -rwxr-xr-x 1 root root 68104 Sep 21 2022 df -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 67548 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Jun 4 01:48 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch -rwxr-xr-x 1 root root 67548 Sep 21 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/25145/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: cmake, debhelper-compat (= 13), dh-python, doctest-dev, help2man, libstb-dev, python3-dev, python3-numpy, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19324 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on doctest-dev; however: Package doctest-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libstb-dev; however: Package libstb-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11 (>= 2.6.0); however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however: Package tao-pegtl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} doctest-dev{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libblas3{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} liblapack3{a} libldap-2.5-0{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libstb-dev{a} libstb0{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} procps{a} pybind11-dev{a} python3{a} python3-attr{a} python3-dev{a} python3-distutils{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pybind11{a} python3-pytest{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tao-pegtl-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libeigen3-dev libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix python3-pygments wget 0 packages upgraded, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 48.5 MB of archives. After unpacking 186 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf liblocale-gettext-perl armhf 1.07-5 [14.9 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B] Get: 12 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libarchive13 armhf 3.6.2-1 [299 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-10 [347 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf librhash0 armhf 1.4.3-3 [146 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libuv1 armhf 1.44.2-1 [126 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf cmake-data all 3.25.1-1 [2026 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf cmake armhf 3.25.1-1 [4263 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 52 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 54 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf python3-distutils all 3.11.2-3 [131 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf dh-python all 5.20230130 [104 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf doctest-dev all 2.4.9~ds-1 [211 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf help2man armhf 1.49.3 [198 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libexpat1-dev armhf 2.5.0-1 [134 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libpython3.11 armhf 3.11.2-6 [1710 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libpython3.11-dev armhf 3.11.2-6 [3518 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libpython3-dev armhf 3.11.2-1+b1 [9556 B] Get: 76 http://deb.debian.org/debian bookworm/main armhf libstb0 armhf 0.0~git20220908.8b5f1f3+ds-1 [176 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libstb-dev armhf 0.0~git20220908.8b5f1f3+ds-1 [556 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf pybind11-dev all 2.10.3-1 [186 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf python3-attr all 22.2.0-1 [65.4 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf python3.11-dev armhf 3.11.2-6 [615 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf python3-dev armhf 3.11.2-1+b1 [26.2 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 83 http://deb.debian.org/debian bookworm/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf python3-pkg-resources all 66.1.1-1 [296 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf python3-numpy armhf 1:1.24.2-1 [4165 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf python3-packaging all 23.0-1 [32.5 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf python3-py all 1.11.0-1 [89.2 kB] Get: 89 http://deb.debian.org/debian bookworm/main armhf python3-pybind11 all 2.10.3-1 [199 kB] Get: 90 http://deb.debian.org/debian bookworm/main armhf python3-pytest all 7.2.1-2 [236 kB] Get: 91 http://deb.debian.org/debian bookworm/main armhf tao-pegtl-dev all 3.2.7-1 [69.4 kB] Fetched 48.5 MB in 14s (3539 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-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 ... 19324 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-5_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.11-minimal:armhf. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.2-6) ... Selecting previously unselected package libexpat1:armhf. 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Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:armhf. Preparing to unpack .../3-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_armhf.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20088 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_armhf.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:armhf. Preparing to unpack .../01-libproc2-0_2%3a4.0.2-3_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.2-3_armhf.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../05-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../08-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../11-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../18-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../19-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package libarchive13:armhf. Preparing to unpack .../20-libarchive13_3.6.2-1_armhf.deb ... Unpacking libarchive13:armhf (3.6.2-1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../21-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../22-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../23-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../24-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../25-libnghttp2-14_1.52.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../26-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../27-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../28-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:armhf. Preparing to unpack .../29-libcurl4_7.88.1-10_armhf.deb ... Unpacking libcurl4:armhf (7.88.1-10) ... Selecting previously unselected package libjsoncpp25:armhf. Preparing to unpack .../30-libjsoncpp25_1.9.5-4_armhf.deb ... Unpacking libjsoncpp25:armhf (1.9.5-4) ... Selecting previously unselected package librhash0:armhf. Preparing to unpack .../31-librhash0_1.4.3-3_armhf.deb ... Unpacking librhash0:armhf (1.4.3-3) ... Selecting previously unselected package libuv1:armhf. Preparing to unpack .../32-libuv1_1.44.2-1_armhf.deb ... Unpacking libuv1:armhf (1.44.2-1) ... Selecting previously unselected package cmake-data. 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Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../40-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../41-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../42-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../43-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../44-gettext_0.21-12_armhf.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../45-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../46-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../47-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../48-python3-lib2to3_3.11.2-3_all.deb ... Unpacking python3-lib2to3 (3.11.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../49-python3-distutils_3.11.2-3_all.deb ... Unpacking python3-distutils (3.11.2-3) ... Selecting previously unselected package dh-python. Preparing to unpack .../50-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package doctest-dev. Preparing to unpack .../51-doctest-dev_2.4.9~ds-1_all.deb ... Unpacking doctest-dev (2.4.9~ds-1) ... Selecting previously unselected package help2man. Preparing to unpack .../52-help2man_1.49.3_armhf.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../53-libblas3_3.11.0-2_armhf.deb ... Unpacking libblas3:armhf (3.11.0-2) ... Selecting previously unselected package libexpat1-dev:armhf. Preparing to unpack .../54-libexpat1-dev_2.5.0-1_armhf.deb ... Unpacking libexpat1-dev:armhf (2.5.0-1) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../55-libgfortran5_12.2.0-14_armhf.deb ... Unpacking libgfortran5:armhf (12.2.0-14) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../56-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../57-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../58-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../59-liblapack3_3.11.0-2_armhf.deb ... Unpacking liblapack3:armhf (3.11.0-2) ... Selecting previously unselected package libpython3.11:armhf. Preparing to unpack .../60-libpython3.11_3.11.2-6_armhf.deb ... Unpacking libpython3.11:armhf (3.11.2-6) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../61-zlib1g-dev_1%3a1.2.13.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Selecting previously unselected package libpython3.11-dev:armhf. Preparing to unpack .../62-libpython3.11-dev_3.11.2-6_armhf.deb ... Unpacking libpython3.11-dev:armhf (3.11.2-6) ... Selecting previously unselected package libpython3-dev:armhf. Preparing to unpack .../63-libpython3-dev_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-dev:armhf (3.11.2-1+b1) ... Selecting previously unselected package libstb0:armhf. Preparing to unpack .../64-libstb0_0.0~git20220908.8b5f1f3+ds-1_armhf.deb ... Unpacking libstb0:armhf (0.0~git20220908.8b5f1f3+ds-1) ... Selecting previously unselected package libstb-dev:armhf. Preparing to unpack .../65-libstb-dev_0.0~git20220908.8b5f1f3+ds-1_armhf.deb ... Unpacking libstb-dev:armhf (0.0~git20220908.8b5f1f3+ds-1) ... Selecting previously unselected package pybind11-dev. Preparing to unpack .../66-pybind11-dev_2.10.3-1_all.deb ... Unpacking pybind11-dev (2.10.3-1) ... Selecting previously unselected package python3-attr. Preparing to unpack .../67-python3-attr_22.2.0-1_all.deb ... Unpacking python3-attr (22.2.0-1) ... Selecting previously unselected package python3.11-dev. Preparing to unpack .../68-python3.11-dev_3.11.2-6_armhf.deb ... Unpacking python3.11-dev (3.11.2-6) ... Selecting previously unselected package python3-dev. Preparing to unpack .../69-python3-dev_3.11.2-1+b1_armhf.deb ... Unpacking python3-dev (3.11.2-1+b1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../70-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../71-python3-more-itertools_8.10.0-2_all.deb ... Unpacking python3-more-itertools (8.10.0-2) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../72-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../73-python3-numpy_1%3a1.24.2-1_armhf.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../74-python3-packaging_23.0-1_all.deb ... Unpacking python3-packaging (23.0-1) ... 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Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up pybind11-dev (2.10.3-1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libuv1:armhf (1.44.2-1) ... Setting up libexpat1-dev:armhf (2.5.0-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:armhf (2:4.0.2-3) ... Setting up libstb0:armhf (0.0~git20220908.8b5f1f3+ds-1) ... Setting up autopoint (0.21-12) ... 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Setting up python3-pytest (7.2.1-2) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Processing triggers for libc-bin (2.36-9) ... 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... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/25145/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/25145/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/gemmi-0.5.7+ds/ && 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 > ../gemmi_0.5.7+ds-2_source.changes dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.5.7+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --buildsystem cmake --with python3 dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem cmake --with python3 dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/gemmi-0.5.7+ds' dh_auto_configure -- -DUSE_PYTHON=1 -DINSTALL_EGG_INFO=OFF cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DUSE_PYTHON=1 -DINSTALL_EGG_INFO=OFF .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Skipping Fortran bindings. Add -D USE_FORTRAN=1 to build them. -- Compiling with C++ standard: 17 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.13") -- Benchmarks not configured. -- The python module will be built. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.11.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.10.3") -- Found pybind11 2.10.3: /usr/include;/usr/include/python3.11 -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/gemmi-0.5.7+ds' dh_auto_build -O--buildsystem=cmake cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/gemmi-0.5.7+ds -B/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/depend make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' cd /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf 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/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/output.dir/DependInfo.cmake --color= make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/depend make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' cd /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/mapcoef.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/build make[3]: Leaving 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CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o -c /build/gemmi-0.5.7+ds/src/mapcoef.cpp /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/input.dir/src/input.cpp.o -MF CMakeFiles/input.dir/src/input.cpp.o.d -o CMakeFiles/input.dir/src/input.cpp.o -c /build/gemmi-0.5.7+ds/src/input.cpp [ 4%] Building CXX object CMakeFiles/options.dir/src/options.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/options.dir/src/options.cpp.o -MF CMakeFiles/options.dir/src/options.cpp.o.d -o CMakeFiles/options.dir/src/options.cpp.o -c /build/gemmi-0.5.7+ds/src/options.cpp [ 7%] Building CXX object CMakeFiles/output.dir/src/output.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/output.dir/src/output.cpp.o -MF CMakeFiles/output.dir/src/output.cpp.o.d -o CMakeFiles/output.dir/src/output.cpp.o -c /build/gemmi-0.5.7+ds/src/output.cpp In file included from /build/gemmi-0.5.7+ds/src/output.cpp:6: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ In file included from /usr/include/c++/12/string:50, from /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:32: /usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]': /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 7%] Built target options make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/depend make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' cd /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/py.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/build make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 7%] Building CXX object CMakeFiles/py.dir/python/mol.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/mol.cpp.o -MF CMakeFiles/py.dir/python/mol.cpp.o.d -o CMakeFiles/py.dir/python/mol.cpp.o -c /build/gemmi-0.5.7+ds/python/mol.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:16, from /build/gemmi-0.5.7+ds/python/mol.cpp:8: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:13, from /build/gemmi-0.5.7+ds/include/gemmi/fileutil.hpp:16, from /build/gemmi-0.5.7+ds/include/gemmi/gz.hpp:14, from /build/gemmi-0.5.7+ds/src/mapcoef.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/cifdoc.hpp:8, from /build/gemmi-0.5.7+ds/include/gemmi/read_cif.hpp:14, from /build/gemmi-0.5.7+ds/src/input.cpp:4: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:358:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:360:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'bool std::none_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/12/bits/stl_algo.h:474:47, inlined from 'bool std::any_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/12/bits/stl_algo.h:493:27, inlined from 'void gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)' at /build/gemmi-0.5.7+ds/include/gemmi/to_mmcif.hpp:612:20: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:335:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 7%] Built target mapcoef [ 9%] Building CXX object CMakeFiles/py.dir/python/gemmi.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/gemmi.cpp.o -MF CMakeFiles/py.dir/python/gemmi.cpp.o.d -o CMakeFiles/py.dir/python/gemmi.cpp.o -c /build/gemmi-0.5.7+ds/python/gemmi.cpp make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 9%] Built target output [ 12%] Building CXX object CMakeFiles/py.dir/python/align.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/align.cpp.o -MF CMakeFiles/py.dir/python/align.cpp.o.d -o CMakeFiles/py.dir/python/align.cpp.o -c /build/gemmi-0.5.7+ds/python/align.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:503:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:518:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:524:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:535:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::impl::apply_hd_mixture(gemmi::Residue*, double)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:448:24, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:771:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 14%] Building CXX object CMakeFiles/py.dir/python/ccp4.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/ccp4.cpp.o -MF CMakeFiles/py.dir/python/ccp4.cpp.o.d -o CMakeFiles/py.dir/python/ccp4.cpp.o -c /build/gemmi-0.5.7+ds/python/ccp4.cpp make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 14%] Built target input make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/depend make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' cd /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/build make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 14%] Building CXX object CMakeFiles/program.dir/src/align.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/align.cpp.o -MF CMakeFiles/program.dir/src/align.cpp.o.d -o CMakeFiles/program.dir/src/align.cpp.o -c /build/gemmi-0.5.7+ds/src/align.cpp [ 14%] Building CXX object CMakeFiles/py.dir/python/chemcomp.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/chemcomp.cpp.o -MF CMakeFiles/py.dir/python/chemcomp.cpp.o.d -o CMakeFiles/py.dir/python/chemcomp.cpp.o -c /build/gemmi-0.5.7+ds/python/chemcomp.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/to_chemcomp.hpp:10, from /build/gemmi-0.5.7+ds/python/chemcomp.cpp:4: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 17%] Building CXX object CMakeFiles/py.dir/python/cif.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/cif.cpp.o -MF CMakeFiles/py.dir/python/cif.cpp.o.d -o CMakeFiles/py.dir/python/cif.cpp.o -c /build/gemmi-0.5.7+ds/python/cif.cpp In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/model.hpp:15, from /build/gemmi-0.5.7+ds/src/align.cpp:5: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Position&}; _Tp = gemmi::Position; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 19%] Building CXX object CMakeFiles/py.dir/python/custom.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/custom.cpp.o -MF CMakeFiles/py.dir/python/custom.cpp.o.d -o CMakeFiles/py.dir/python/custom.cpp.o -c /build/gemmi-0.5.7+ds/python/custom.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Position; _Alloc = std::allocator]', inlined from 'void gemmi::prepare_positions_for_superposition(std::vector&, std::vector&, ConstResidueSpan, ConstResidueSpan, PolymerType, SupSelect, char, std::vector*)' at /build/gemmi-0.5.7+ds/include/gemmi/align.hpp:188:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Position; _Alloc = std::allocator]', inlined from 'void gemmi::prepare_positions_for_superposition(std::vector&, std::vector&, ConstResidueSpan, ConstResidueSpan, PolymerType, SupSelect, char, std::vector*)' at /build/gemmi-0.5.7+ds/include/gemmi/align.hpp:189:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Position; _Alloc = std::allocator]', inlined from 'void gemmi::prepare_positions_for_superposition(std::vector&, std::vector&, ConstResidueSpan, ConstResidueSpan, PolymerType, SupSelect, char, std::vector*)' at /build/gemmi-0.5.7+ds/include/gemmi/align.hpp:196:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Position; _Alloc = std::allocator]', inlined from 'void gemmi::prepare_positions_for_superposition(std::vector&, std::vector&, ConstResidueSpan, ConstResidueSpan, PolymerType, SupSelect, char, std::vector*)' at /build/gemmi-0.5.7+ds/include/gemmi/align.hpp:197:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 21%] Building CXX object CMakeFiles/program.dir/src/blobs.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/blobs.cpp.o -MF CMakeFiles/program.dir/src/blobs.cpp.o.d -o CMakeFiles/program.dir/src/blobs.cpp.o -c /build/gemmi-0.5.7+ds/src/blobs.cpp [ 21%] Building CXX object CMakeFiles/py.dir/python/elem.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/elem.cpp.o -MF CMakeFiles/py.dir/python/elem.cpp.o.d -o CMakeFiles/py.dir/python/elem.cpp.o -c /build/gemmi-0.5.7+ds/python/elem.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/gemmi-0.5.7+ds/src/blobs.cpp:4: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Blob; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const BlobCriteria&, bool):: >]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/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&, const BlobCriteria&, bool):: >]': /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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&, const BlobCriteria&, bool):: >]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/grid.hpp:15, from /build/gemmi-0.5.7+ds/include/gemmi/blob.hpp:13, from /build/gemmi-0.5.7+ds/src/blobs.cpp:6: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:358:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:360:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Blob&}; _Tp = gemmi::Blob; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Fractional&}; _Tp = gemmi::Fractional; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Fractional; _Alloc = std::allocator]', inlined from 'void gemmi::NeighborSearch::add_site(const gemmi::SmallStructure::Site&, int)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:286:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 24%] Building CXX object CMakeFiles/py.dir/python/grid.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/grid.cpp.o -MF CMakeFiles/py.dir/python/grid.cpp.o.d -o CMakeFiles/py.dir/python/grid.cpp.o -c /build/gemmi-0.5.7+ds/python/grid.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:367:20, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:183:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'void gemmi::expand_ncs(Structure&, HowToNameCopiedChain)' at /build/gemmi-0.5.7+ds/include/gemmi/assembly.hpp:349:37: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/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&, const BlobCriteria&, bool):: >]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Blob; _Alloc = std::allocator]', inlined from 'std::vector gemmi::find_blobs_by_flood_fill(const Grid&, const BlobCriteria&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/blob.hpp:132:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const BlobCriteria&, bool):: >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = gemmi::find_blobs_by_flood_fill(const Grid&, const BlobCriteria&, bool)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'std::vector gemmi::find_blobs_by_flood_fill(const Grid&, const BlobCriteria&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/blob.hpp:134:12: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const BlobCriteria&, bool):: >]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const BlobCriteria&, bool):: >]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = gemmi::find_blobs_by_flood_fill(const Grid&, const BlobCriteria&, bool)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'std::vector gemmi::find_blobs_by_flood_fill(const Grid&, const BlobCriteria&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/blob.hpp:134:12: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 26%] Building CXX object CMakeFiles/py.dir/python/hkl.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -Wno-psabi -MD -MT CMakeFiles/py.dir/python/hkl.cpp.o -MF CMakeFiles/py.dir/python/hkl.cpp.o.d -o CMakeFiles/py.dir/python/hkl.cpp.o -c /build/gemmi-0.5.7+ds/python/hkl.cpp [ 29%] Building CXX object CMakeFiles/program.dir/src/cif2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/cif2mtz.cpp.o -MF CMakeFiles/program.dir/src/cif2mtz.cpp.o.d -o CMakeFiles/program.dir/src/cif2mtz.cpp.o -c /build/gemmi-0.5.7+ds/src/cif2mtz.cpp [ 31%] Building CXX object CMakeFiles/py.dir/python/meta.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/meta.cpp.o -MF CMakeFiles/py.dir/python/meta.cpp.o.d -o CMakeFiles/py.dir/python/meta.cpp.o -c /build/gemmi-0.5.7+ds/python/meta.cpp In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/cifdoc.hpp:8, from /build/gemmi-0.5.7+ds/include/gemmi/read_cif.hpp:14, from /build/gemmi-0.5.7+ds/src/cif2mtz.cpp:12: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Mtz::Dataset& gemmi::Mtz::add_dataset(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:930:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]', inlined from 'std::vector gemmi::as_refln_blocks(std::vector&&)' at /build/gemmi-0.5.7+ds/include/gemmi/refln.hpp:149:22: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object CMakeFiles/py.dir/python/monlib.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/monlib.cpp.o -MF CMakeFiles/py.dir/python/monlib.cpp.o.d -o CMakeFiles/py.dir/python/monlib.cpp.o -c /build/gemmi-0.5.7+ds/python/monlib.cpp [ 34%] Building CXX object CMakeFiles/program.dir/src/cif2json.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/cif2json.cpp.o -MF CMakeFiles/program.dir/src/cif2json.cpp.o.d -o CMakeFiles/program.dir/src/cif2json.cpp.o -c /build/gemmi-0.5.7+ds/src/cif2json.cpp [ 36%] Building CXX object CMakeFiles/py.dir/python/mtz.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -Wno-psabi -MD -MT CMakeFiles/py.dir/python/mtz.cpp.o -MF CMakeFiles/py.dir/python/mtz.cpp.o.d -o CMakeFiles/py.dir/python/mtz.cpp.o -c /build/gemmi-0.5.7+ds/python/mtz.cpp [ 36%] Building CXX object CMakeFiles/program.dir/src/contact.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/contact.cpp.o -MF CMakeFiles/program.dir/src/contact.cpp.o.d -o CMakeFiles/program.dir/src/contact.cpp.o -c /build/gemmi-0.5.7+ds/src/contact.cpp [ 39%] Building CXX object CMakeFiles/py.dir/python/read.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/read.cpp.o -MF CMakeFiles/py.dir/python/read.cpp.o.d -o CMakeFiles/py.dir/python/read.cpp.o -c /build/gemmi-0.5.7+ds/python/read.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/smcif.hpp:12, from /build/gemmi-0.5.7+ds/python/read.cpp:7: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/model.hpp:15, from /build/gemmi-0.5.7+ds/include/gemmi/contact.hpp:8, from /build/gemmi-0.5.7+ds/src/contact.cpp:8: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Fractional&}; _Tp = gemmi::Fractional; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Fractional; _Alloc = std::allocator]', inlined from 'void gemmi::NeighborSearch::add_site(const gemmi::SmallStructure::Site&, int)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:286:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:367:20, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:183:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:197:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'void gemmi::transform_to_assembly(Structure&, const std::string&, HowToNameCopiedChain, std::ostream*)' at /build/gemmi-0.5.7+ds/include/gemmi/assembly.hpp:249:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 39%] Building CXX object CMakeFiles/py.dir/python/recgrid.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -Wno-psabi -MD -MT CMakeFiles/py.dir/python/recgrid.cpp.o -MF CMakeFiles/py.dir/python/recgrid.cpp.o.d -o CMakeFiles/py.dir/python/recgrid.cpp.o -c /build/gemmi-0.5.7+ds/python/recgrid.cpp [ 41%] Building CXX object CMakeFiles/program.dir/src/contents.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/contents.cpp.o -MF CMakeFiles/program.dir/src/contents.cpp.o.d -o CMakeFiles/program.dir/src/contents.cpp.o -c /build/gemmi-0.5.7+ds/src/contents.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:16, from /build/gemmi-0.5.7+ds/src/contents.cpp:13: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 43%] Building CXX object CMakeFiles/py.dir/python/scaling.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/scaling.cpp.o -MF CMakeFiles/py.dir/python/scaling.cpp.o.d -o CMakeFiles/py.dir/python/scaling.cpp.o -c /build/gemmi-0.5.7+ds/python/scaling.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /build/gemmi-0.5.7+ds/include/gemmi/symmetry.hpp:16, from /build/gemmi-0.5.7+ds/src/contents.cpp:8: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::impl::parse_cid(const std::string&, gemmi::Selection&)' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:513:38: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void {anonymous}::print_bfactor_info(const gemmi::Model&)' at /build/gemmi-0.5.7+ds/src/contents.cpp:195:29, inlined from 'int contents_main(int, char**)' at /build/gemmi-0.5.7+ds/src/contents.cpp:229:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object CMakeFiles/program.dir/src/convert.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/convert.cpp.o -MF CMakeFiles/program.dir/src/convert.cpp.o.d -o CMakeFiles/program.dir/src/convert.cpp.o -c /build/gemmi-0.5.7+ds/src/convert.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:16, from /build/gemmi-0.5.7+ds/src/convert.cpp:16: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 48%] Building CXX object CMakeFiles/py.dir/python/search.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/search.cpp.o -MF CMakeFiles/py.dir/python/search.cpp.o.d -o CMakeFiles/py.dir/python/search.cpp.o -c /build/gemmi-0.5.7+ds/python/search.cpp [ 51%] Building CXX object CMakeFiles/py.dir/python/sf.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sf.cpp.o -MF CMakeFiles/py.dir/python/sf.cpp.o.d -o CMakeFiles/py.dir/python/sf.cpp.o -c /build/gemmi-0.5.7+ds/python/sf.cpp [ 51%] Building CXX object CMakeFiles/py.dir/python/sym.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sym.cpp.o -MF CMakeFiles/py.dir/python/sym.cpp.o.d -o CMakeFiles/py.dir/python/sym.cpp.o -c /build/gemmi-0.5.7+ds/python/sym.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/it92.hpp:16, from /build/gemmi-0.5.7+ds/python/sf.cpp:6: /build/gemmi-0.5.7+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 5; Real = double]': /build/gemmi-0.5.7+ds/include/gemmi/dencalc.hpp:19:54: required from 'double gemmi::determine_cutoff_radius(double, const PrecalExpSum&, double) [with PrecalExpSum = ExpSum<5, double>]' /build/gemmi-0.5.7+ds/include/gemmi/dencalc.hpp:130:35: required from 'double gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, double) const [with int N = 5; Table = gemmi::IT92; Real = float; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<4, 1, double>]' /build/gemmi-0.5.7+ds/python/sf.cpp:63:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' /build/gemmi-0.5.7+ds/python/sf.cpp:86:20: required from here /build/gemmi-0.5.7+ds/include/gemmi/formfact.hpp:28:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 28 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/cifdoc.hpp:8, from /build/gemmi-0.5.7+ds/include/gemmi/to_cif.hpp:9, from /build/gemmi-0.5.7+ds/src/convert.cpp:3: /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 189 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = Selection::remove_not_selected(gemmi::Residue&) const::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:10, inlined from 'void gemmi::Selection::remove_not_selected(T&) const [with T = gemmi::Residue]' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:289:21, inlined from 'void gemmi::Selection::remove_not_selected(T&) const [with T = gemmi::Chain]' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:291:26, inlined from 'void gemmi::Selection::remove_not_selected(T&) const [with T = gemmi::Model]' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:291:26, inlined from 'void gemmi::Selection::remove_not_selected(T&) const [with T = gemmi::Structure]' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:291:26: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = remove_hydrogens(Residue&)::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:10, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Residue]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:48:19, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Chain]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Model]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Structure]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:358:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:360:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::BasicRefinementInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ReflectionsInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Fractional&}; _Tp = gemmi::Fractional; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Fractional; _Alloc = std::allocator]', inlined from 'void gemmi::NeighborSearch::add_site(const gemmi::SmallStructure::Site&, int)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:286:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = Selection::remove_selected(gemmi::Residue&) const::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:10, inlined from 'void gemmi::Selection::remove_selected(gemmi::Residue&) const' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:284:23, inlined from 'void gemmi::Selection::remove_selected(T&) const [with T = gemmi::Chain]' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:275:24, inlined from 'void gemmi::Selection::remove_selected(T&) const [with T = gemmi::Model]' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:275:24: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 53%] Building CXX object CMakeFiles/py.dir/python/topo.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/topo.cpp.o -MF CMakeFiles/py.dir/python/topo.cpp.o.d -o CMakeFiles/py.dir/python/topo.cpp.o -c /build/gemmi-0.5.7+ds/python/topo.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/crd.hpp:13, from /build/gemmi-0.5.7+ds/python/topo.cpp:5: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:367:20, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:183:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark_200_230_240(const char*, gemmi::Metadata&, std::string*&)' at /build/gemmi-0.5.7+ds/include/gemmi/remarks.hpp:436:33: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark_200_230_240(const char*, gemmi::Metadata&, std::string*&)' at /build/gemmi-0.5.7+ds/include/gemmi/remarks.hpp:439:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark_200_230_240(const char*, gemmi::Metadata&, std::string*&)' at /build/gemmi-0.5.7+ds/include/gemmi/remarks.hpp:441:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::ReflectionsInfo; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark_200_230_240(const char*, gemmi::Metadata&, std::string*&)' at /build/gemmi-0.5.7+ds/include/gemmi/remarks.hpp:452:52: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'void gemmi::expand_ncs(Structure&, HowToNameCopiedChain)' at /build/gemmi-0.5.7+ds/include/gemmi/assembly.hpp:349:37: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 56%] Building CXX object CMakeFiles/py.dir/python/unitcell.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/unitcell.cpp.o -MF CMakeFiles/py.dir/python/unitcell.cpp.o.d -o CMakeFiles/py.dir/python/unitcell.cpp.o -c /build/gemmi-0.5.7+ds/python/unitcell.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::impl::parse_cid(const std::string&, gemmi::Selection&)' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:513:38: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const char*&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const char*&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::add_restraint_count_weight(gemmi::RefinementInfo&, const char*, const char*)' at /build/gemmi-0.5.7+ds/include/gemmi/remarks.hpp:94:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]', inlined from 'T& gemmi::impl::find_or_add(std::vector&, const std::string&) [with T = gemmi::RefinementInfo::Restr]' at /build/gemmi-0.5.7+ds/include/gemmi/model.hpp:42:19, inlined from 'T& gemmi::impl::find_or_add(std::vector&, const std::string&) [with T = gemmi::RefinementInfo::Restr]' at /build/gemmi-0.5.7+ds/include/gemmi/model.hpp:39:4: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark3_line(const char*, gemmi::Metadata&, std::string*&)' at /build/gemmi-0.5.7+ds/include/gemmi/remarks.hpp:257:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark3_line(const char*, gemmi::Metadata&, std::string*&)' at /build/gemmi-0.5.7+ds/include/gemmi/remarks.hpp:313:35: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::BasicRefinementInfo; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark3_line(const char*, gemmi::Metadata&, std::string*&)' at /build/gemmi-0.5.7+ds/include/gemmi/remarks.hpp:317:49: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object CMakeFiles/py.dir/python/write.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/write.cpp.o -MF CMakeFiles/py.dir/python/write.cpp.o.d -o CMakeFiles/py.dir/python/write.cpp.o -c /build/gemmi-0.5.7+ds/python/write.cpp In file included from /build/gemmi-0.5.7+ds/python/write.cpp:4: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'void gemmi::transform_to_assembly(Structure&, const std::string&, HowToNameCopiedChain, std::ostream*)' at /build/gemmi-0.5.7+ds/include/gemmi/assembly.hpp:249:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = trim_to_alanine(Residue&)::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:10, inlined from 'bool gemmi::trim_to_alanine(Residue&)' at /build/gemmi-0.5.7+ds/include/gemmi/polyheur.hpp:342:19, inlined from 'void gemmi::trim_to_alanine(Chain&)' at /build/gemmi-0.5.7+ds/include/gemmi/polyheur.hpp:353:20, inlined from 'void {anonymous}::convert(gemmi::Structure&, const std::string&, gemmi::CoorFormat, const std::vector&)' at /build/gemmi-0.5.7+ds/src/convert.cpp:324:24, inlined from 'int convert_main(int, char**)' at /build/gemmi-0.5.7+ds/src/convert.cpp:409:12: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object CMakeFiles/program.dir/src/fprime.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/fprime.cpp.o -MF CMakeFiles/program.dir/src/fprime.cpp.o.d -o CMakeFiles/program.dir/src/fprime.cpp.o -c /build/gemmi-0.5.7+ds/src/fprime.cpp In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/math.hpp:14, from /build/gemmi-0.5.7+ds/src/fprime.cpp:5: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'int fprime_main(int, char**)' at /build/gemmi-0.5.7+ds/src/fprime.cpp:49:25: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'int fprime_main(int, char**)' at /build/gemmi-0.5.7+ds/src/fprime.cpp:52:25: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building CXX object CMakeFiles/program.dir/src/grep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/grep.cpp.o -MF CMakeFiles/program.dir/src/grep.cpp.o.d -o CMakeFiles/program.dir/src/grep.cpp.o -c /build/gemmi-0.5.7+ds/src/grep.cpp [ 60%] Building CXX object CMakeFiles/program.dir/src/h.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/h.cpp.o -MF CMakeFiles/program.dir/src/h.cpp.o.d -o CMakeFiles/program.dir/src/h.cpp.o -c /build/gemmi-0.5.7+ds/src/h.cpp [ 63%] Building CXX object CMakeFiles/program.dir/src/json2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/json2cif.cpp.o -MF CMakeFiles/program.dir/src/json2cif.cpp.o.d -o CMakeFiles/program.dir/src/json2cif.cpp.o -c /build/gemmi-0.5.7+ds/src/json2cif.cpp [ 65%] Linking CXX shared module gemmi.cpython-311-arm-linux-gnueabihf.so /usr/bin/cmake -E cmake_link_script CMakeFiles/py.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -flto -Wl,-z,relro -shared -o gemmi.cpython-311-arm-linux-gnueabihf.so CMakeFiles/py.dir/python/mol.cpp.o CMakeFiles/py.dir/python/gemmi.cpp.o CMakeFiles/py.dir/python/align.cpp.o CMakeFiles/py.dir/python/ccp4.cpp.o CMakeFiles/py.dir/python/chemcomp.cpp.o CMakeFiles/py.dir/python/cif.cpp.o CMakeFiles/py.dir/python/custom.cpp.o CMakeFiles/py.dir/python/elem.cpp.o CMakeFiles/py.dir/python/grid.cpp.o CMakeFiles/py.dir/python/hkl.cpp.o CMakeFiles/py.dir/python/meta.cpp.o CMakeFiles/py.dir/python/monlib.cpp.o CMakeFiles/py.dir/python/mtz.cpp.o CMakeFiles/py.dir/python/read.cpp.o CMakeFiles/py.dir/python/recgrid.cpp.o CMakeFiles/py.dir/python/scaling.cpp.o CMakeFiles/py.dir/python/search.cpp.o CMakeFiles/py.dir/python/sf.cpp.o CMakeFiles/py.dir/python/sym.cpp.o CMakeFiles/py.dir/python/topo.cpp.o CMakeFiles/py.dir/python/unitcell.cpp.o CMakeFiles/py.dir/python/write.cpp.o /usr/lib/arm-linux-gnueabihf/libz.so [ 65%] Building CXX object CMakeFiles/program.dir/src/main.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/main.cpp.o -MF CMakeFiles/program.dir/src/main.cpp.o.d -o CMakeFiles/program.dir/src/main.cpp.o -c /build/gemmi-0.5.7+ds/src/main.cpp [ 68%] Building CXX object CMakeFiles/program.dir/src/map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/map.cpp.o -MF CMakeFiles/program.dir/src/map.cpp.o.d -o CMakeFiles/program.dir/src/map.cpp.o -c /build/gemmi-0.5.7+ds/src/map.cpp In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/cifdoc.hpp:8, from /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:11, from /build/gemmi-0.5.7+ds/src/h.cpp:7: /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 189 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/string:50, from /usr/include/c++/12/stdexcept:39, from /build/gemmi-0.5.7+ds/src/h.cpp:5: /usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]': /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algobase.h: In function '_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(Residue&):: >]': /usr/include/c++/12/bits/stl_algobase.h:2131:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2131 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h:2131:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/algorithm:61, from /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:8, from /build/gemmi-0.5.7+ds/include/gemmi/cifdoc.hpp:11: /usr/include/c++/12/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++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Atom; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ [ 70%] Building CXX object CMakeFiles/program.dir/src/map2sf.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/map2sf.cpp.o -MF CMakeFiles/program.dir/src/map2sf.cpp.o.d -o CMakeFiles/program.dir/src/map2sf.cpp.o -c /build/gemmi-0.5.7+ds/src/map2sf.cpp [ 70%] Building CXX object CMakeFiles/program.dir/src/mask.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/mask.cpp.o -MF CMakeFiles/program.dir/src/mask.cpp.o.d -o CMakeFiles/program.dir/src/mask.cpp.o -c /build/gemmi-0.5.7+ds/src/mask.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:358:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:360:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::add_hydrogens_without_positions(const ChemComp&, Residue&)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:36:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Angle&}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::get_plane(const std::string&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::get_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:245:24, inlined from 'gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:250:48: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:253:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Torsion&}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom}; _Tp = gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom}; _Tp = gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::place_hydrogens(const Topo&, const Atom&)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:152:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/grid.hpp:15, from /build/gemmi-0.5.7+ds/src/map2sf.cpp:12: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object CMakeFiles/program.dir/src/merge.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/merge.cpp.o -MF CMakeFiles/program.dir/src/merge.cpp.o.d -o CMakeFiles/program.dir/src/merge.cpp.o -c /build/gemmi-0.5.7+ds/src/merge.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/mtz2cif.hpp:24, from /build/gemmi-0.5.7+ds/src/merge.cpp:14: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'void gemmi::impl::read_connectivity(gemmi::cif::Block&, gemmi::Structure&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:240:32: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:284:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:292:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:335:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Bond&}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:421:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:453:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:479:41: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::get_plane(const std::string&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::get_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:245:24, inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:535:40: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:13, from /build/gemmi-0.5.7+ds/include/gemmi/fileutil.hpp:16, from /build/gemmi-0.5.7+ds/include/gemmi/gz.hpp:14, from /build/gemmi-0.5.7+ds/src/merge.cpp:13: /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 189 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/algorithm:61, from /build/gemmi-0.5.7+ds/src/merge.cpp:8: /usr/include/c++/12/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++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Intensities::Refl; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Intensities::Refl; F = Intensities::remove_systematic_absences()::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:10: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/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++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', inlined from 'void gemmi::Mtz::read_main_headers(Stream&) [with Stream = gemmi::FileStream]' at /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:621:32: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:503:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:518:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:524:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:535:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::NcsOp; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:629:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:769:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::impl::apply_hd_mixture(gemmi::Residue*, double)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:448:24, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:771:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ lto-wrapper: warning: using serial compilation of 112 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; _Tp = gemmi::Restraints::Bond]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; _Tp = gemmi::Restraints::Angle]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; _Tp = gemmi::Restraints::Torsion]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; _Tp = gemmi::Restraints::Plane]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {int}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; _Tp = gemmi::Restraints::Bond]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; _Tp = gemmi::Restraints::Angle]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; _Tp = gemmi::Restraints::Torsion]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; _Tp = gemmi::Restraints::Plane]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::MtzDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:485:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::MtzDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:488:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_unmerged_intensities_from_xds(const gemmi::XdsAscii&)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:432:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_data(const DataProxy&, size_t, size_t) [with DataProxy = gemmi::MtzDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:465:19, inlined from 'void gemmi::Intensities::read_mean_intensities_from_mtz(const gemmi::Mtz&)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:297:14: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::remove_hydrogens(Residue&)::]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = remove_hydrogens(Residue&)::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:25, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Residue]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:48:19, inlined from 'std::unique_ptr gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:402:27: /usr/include/c++/12/bits/stl_algo.h:877:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 877 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 878 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = remove_hydrogens(Residue&)::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:10, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Residue]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:48:19, inlined from 'std::unique_ptr gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:402:27: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'std::unique_ptr gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:424:20: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'std::unique_ptr gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:424:20: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_unmerged_intensities_from_mtz(const gemmi::Mtz&)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:280:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::remove_hydrogens(Residue&)::]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = remove_hydrogens(Residue&)::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:25, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Residue]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:48:19, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Chain]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Model]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Structure]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21, inlined from 'int h_main(int, char**)' at /build/gemmi-0.5.7+ds/src/h.cpp:106:30: /usr/include/c++/12/bits/stl_algo.h:877:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 877 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 878 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = remove_hydrogens(Residue&)::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:10, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Residue]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:48:19, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Chain]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Model]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21, inlined from 'void gemmi::remove_hydrogens(T&) [with T = Structure]' at /build/gemmi-0.5.7+ds/include/gemmi/modify.hpp:45:21, inlined from 'int h_main(int, char**)' at /build/gemmi-0.5.7+ds/src/h.cpp:106:30: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:55:23, inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::MaybeGzipped::GzStream]' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:153:48: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::MaybeGzipped::GzStream]' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:191:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:55:23, inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:153:48: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:191:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object CMakeFiles/program.dir/src/mondiff.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/mondiff.cpp.o -MF CMakeFiles/program.dir/src/mondiff.cpp.o.d -o CMakeFiles/program.dir/src/mondiff.cpp.o -c /build/gemmi-0.5.7+ds/src/mondiff.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_data(const DataProxy&, size_t, size_t) [with DataProxy = gemmi::ReflnDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:465:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::ReflnDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:485:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::ReflnDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:488:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 78%] Building CXX object CMakeFiles/program.dir/src/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wno-psabi -MD -MT CMakeFiles/program.dir/src/mtz.cpp.o -MF CMakeFiles/program.dir/src/mtz.cpp.o.d -o CMakeFiles/program.dir/src/mtz.cpp.o -c /build/gemmi-0.5.7+ds/src/mtz.cpp In file included from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/set:60, from /build/gemmi-0.5.7+ds/src/mondiff.cpp:7: /usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&):: >]': /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]', inlined from 'std::vector gemmi::as_refln_blocks(std::vector&&)' at /build/gemmi-0.5.7+ds/include/gemmi/refln.hpp:149:22: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void gemmi::Intensities::sort()' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:200:26, inlined from 'void gemmi::Intensities::merge_in_place(gemmi::DataType)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:210:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void gemmi::Intensities::sort()' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:200:26, inlined from 'void gemmi::Intensities::merge_in_place(gemmi::DataType)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:210:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void gemmi::Intensities::merge_in_place(gemmi::DataType)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:234:15: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&, const AtomId&, const AtomId&):: >]': /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:10, from /build/gemmi-0.5.7+ds/src/mondiff.cpp:8: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void gemmi::Intensities::sort()' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:200:26, inlined from 'void {anonymous}::compare_intensities(gemmi::Intensities&, gemmi::Intensities&, bool)' at /build/gemmi-0.5.7+ds/src/merge.cpp:222:11, inlined from 'int merge_main(int, char**)' at /build/gemmi-0.5.7+ds/src/merge.cpp:349:26: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void gemmi::Intensities::sort()' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:200:26, inlined from 'void {anonymous}::compare_intensities(gemmi::Intensities&, gemmi::Intensities&, bool)' at /build/gemmi-0.5.7+ds/src/merge.cpp:222:11, inlined from 'int merge_main(int, char**)' at /build/gemmi-0.5.7+ds/src/merge.cpp:349:26: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:487:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:494:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:502:29: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:253:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:535:54: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&):: >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::find_bond(const AtomId&, const AtomId&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::find_bond(const T&, const T&) [with T = AtomId]' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:143:24, inlined from 'std::vector::const_iterator gemmi::Restraints::find_bond(const T&, const T&) const [with T = AtomId]' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:149:52, inlined from 'void {anonymous}::compare_chemcomps(const gemmi::ChemComp&, const gemmi::ChemComp&, const MinDelta&)' at /build/gemmi-0.5.7+ds/src/mondiff.cpp:95:30, inlined from 'int mondiff_main(int, char**)' at /build/gemmi-0.5.7+ds/src/mondiff.cpp:240:22: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&):: >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::find_bond(const AtomId&, const AtomId&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::find_bond(const T&, const T&) [with T = AtomId]' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:143:24, inlined from 'std::vector::const_iterator gemmi::Restraints::find_bond(const T&, const T&) const [with T = AtomId]' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:149:52, inlined from 'void {anonymous}::compare_chemcomps(const gemmi::ChemComp&, const gemmi::ChemComp&, const MinDelta&)' at /build/gemmi-0.5.7+ds/src/mondiff.cpp:112:25, inlined from 'int mondiff_main(int, char**)' at /build/gemmi-0.5.7+ds/src/mondiff.cpp:240:22: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&, const AtomId&, const AtomId&):: >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::find_torsion(const AtomId&, const AtomId&, const AtomId&, const AtomId&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::find_torsion(const T&, const T&, const T&, const T&) [with T = AtomId]' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:217:24, inlined from 'std::vector::const_iterator gemmi::Restraints::find_torsion(const T&, const T&, const T&, const T&) const [with T = AtomId]' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:225:55, inlined from 'void {anonymous}::compare_chemcomps(const gemmi::ChemComp&, const gemmi::ChemComp&, const MinDelta&)' at /build/gemmi-0.5.7+ds/src/mondiff.cpp:135:33, inlined from 'int mondiff_main(int, char**)' at /build/gemmi-0.5.7+ds/src/mondiff.cpp:240:22: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&, const AtomId&, const AtomId&):: >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::find_torsion(const AtomId&, const AtomId&, const AtomId&, const AtomId&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::find_torsion(const T&, const T&, const T&, const T&) [with T = AtomId]' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:217:24, inlined from 'std::vector::const_iterator gemmi::Restraints::find_torsion(const T&, const T&, const T&, const T&) const [with T = AtomId]' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:225:55, inlined from 'void {anonymous}::compare_chemcomps(const gemmi::ChemComp&, const gemmi::ChemComp&, const MinDelta&)' at /build/gemmi-0.5.7+ds/src/mondiff.cpp:148:28, inlined from 'int mondiff_main(int, char**)' at /build/gemmi-0.5.7+ds/src/mondiff.cpp:240:22: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 78%] Building CXX object CMakeFiles/program.dir/src/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/mtz2cif.cpp.o -MF CMakeFiles/program.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/program.dir/src/mtz2cif.cpp.o -c /build/gemmi-0.5.7+ds/src/mtz2cif.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/mtz2cif.hpp:24, from /build/gemmi-0.5.7+ds/src/mtz2cif.cpp:8: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 80%] Building CXX object CMakeFiles/program.dir/src/prep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/prep.cpp.o -MF CMakeFiles/program.dir/src/prep.cpp.o.d -o CMakeFiles/program.dir/src/prep.cpp.o -c /build/gemmi-0.5.7+ds/src/prep.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/crd.hpp:13, from /build/gemmi-0.5.7+ds/src/prep.cpp:7: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/asudata.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/mtz2cif.hpp:18: /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 189 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/algorithm:61, from /build/gemmi-0.5.7+ds/include/gemmi/mtz2cif.hpp:17: /usr/include/c++/12/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++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Intensities::Refl; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Intensities::Refl; F = Intensities::remove_systematic_absences()::]' at /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:263:10: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object CMakeFiles/program.dir/src/reindex.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/reindex.cpp.o -MF CMakeFiles/program.dir/src/reindex.cpp.o.d -o CMakeFiles/program.dir/src/reindex.cpp.o -c /build/gemmi-0.5.7+ds/src/reindex.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {int}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::MtzDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:485:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::MtzDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:488:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:50, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/gemmi-0.5.7+ds/src/prep.cpp:5: /usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]': /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_unmerged_intensities_from_xds(const gemmi::XdsAscii&)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:432:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_data(const DataProxy&, size_t, size_t) [with DataProxy = gemmi::MtzDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:465:19, inlined from 'void gemmi::Intensities::read_mean_intensities_from_mtz(const gemmi::Mtz&)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:297:14: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_unmerged_intensities_from_mtz(const gemmi::Mtz&)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:280:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/algorithm:61, from /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:8, from /build/gemmi-0.5.7+ds/include/gemmi/cifdoc.hpp:11, from /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:11, from /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/crd.hpp:9: /usr/include/c++/12/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++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Atom; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:55:23, inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::MaybeGzipped::GzStream]' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:153:48: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::MaybeGzipped::GzStream]' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:191:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:55:23, inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:153:48: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/gemmi-0.5.7+ds/include/gemmi/xds_ascii.hpp:191:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_data(const DataProxy&, size_t, size_t) [with DataProxy = gemmi::ReflnDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:465:19, inlined from 'void gemmi::Intensities::read_mean_intensities_from_mmcif(const gemmi::ReflnBlock&)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:360:14: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::ReflnDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:485:19: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:459:21, inlined from 'void gemmi::Intensities::add_if_valid(const gemmi::Miller&, short int, double, double)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:455:8, inlined from 'void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::ReflnDataProxy]' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:488:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:17, from /build/gemmi-0.5.7+ds/include/gemmi/reindex.hpp:9, from /build/gemmi-0.5.7+ds/src/reindex.cpp:12: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void gemmi::Intensities::sort()' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:200:26, inlined from 'void gemmi::Intensities::merge_in_place(gemmi::DataType)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:210:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void gemmi::Intensities::sort()' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:200:26, inlined from 'void gemmi::Intensities::merge_in_place(gemmi::DataType)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:210:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void gemmi::Intensities::merge_in_place(gemmi::DataType)' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:234:15: /usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void gemmi::Intensities::sort()' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:200:26, inlined from 'bool gemmi::validate_merged_intensities(Intensities&, Intensities&, bool, std::ostream&)' at /build/gemmi-0.5.7+ds/include/gemmi/mtz2cif.hpp:491:10: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void gemmi::Intensities::sort()' at /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:200:26, inlined from 'bool gemmi::validate_merged_intensities(Intensities&, Intensities&, bool, std::ostream&)' at /build/gemmi-0.5.7+ds/include/gemmi/mtz2cif.hpp:491:10: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Angle&}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::add_hydrogens_without_positions(const ChemComp&, Residue&)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:36:30: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Fractional&}; _Tp = gemmi::Fractional; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object CMakeFiles/program.dir/src/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/residues.cpp.o -MF CMakeFiles/program.dir/src/residues.cpp.o.d -o CMakeFiles/program.dir/src/residues.cpp.o -c /build/gemmi-0.5.7+ds/src/residues.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Fractional; _Alloc = std::allocator]', inlined from 'void gemmi::NeighborSearch::add_site(const gemmi::SmallStructure::Site&, int)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:286:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:16, from /build/gemmi-0.5.7+ds/src/residues.cpp:5: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:367:20, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:183:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:197:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::get_plane(const std::string&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::get_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:245:24, inlined from 'gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:250:48: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:253:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object CMakeFiles/program.dir/src/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/rmsz.cpp.o -MF CMakeFiles/program.dir/src/rmsz.cpp.o.d -o CMakeFiles/program.dir/src/rmsz.cpp.o -c /build/gemmi-0.5.7+ds/src/rmsz.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Torsion&}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom}; _Tp = gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom}; _Tp = gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::place_hydrogens(const Topo&, const Atom&)::BondedAtom; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::place_hydrogens(const Topo&, const Atom&)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:152:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from '{anonymous}::assign_connections(gemmi::Model&, gemmi::Structure&)::' at /build/gemmi-0.5.7+ds/src/prep.cpp:83:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Bond&}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:50, from /build/gemmi-0.5.7+ds/src/residues.cpp:4: /usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_negate >]': /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:421:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:453:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:479:41: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::get_plane(const std::string&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::get_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:245:24, inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:535:40: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:13, from /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:13: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::impl::parse_cid(const std::string&, gemmi::Selection&)' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:513:38: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/string:50, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/gemmi-0.5.7+ds/src/rmsz.cpp:5: /usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]': /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/algorithm:61, from /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:8: In function '_InputIterator std::__find_if_not(_InputIterator, _InputIterator, _Predicate) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if_not(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/12/bits/stl_algo.h:516:32, inlined from 'bool std::all_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/12/bits/stl_algo.h:456:40, inlined from 'bool gemmi::Selection::matches(const gemmi::Atom&) const' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:199:23, inlined from 'bool gemmi::FilterIterPolicy::matches(std::size_t) const [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:187:62, inlined from 'gemmi::FilterIterPolicy::FilterIterPolicy(const Filter*, Vector*, std::size_t) [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:184:44, inlined from 'gemmi::FilterProxy::iterator gemmi::FilterProxy::begin() [with Filter = gemmi::Selection; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:207:48, inlined from 'int residues_main(int, char**)' at /build/gemmi-0.5.7+ds/src/residues.cpp:154:41: /usr/include/c++/12/bits/stl_algo.h:109:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 109 | return std::__find_if(__first, __last, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 110 | __gnu_cxx::__ops::__negate(__pred), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_InputIterator std::__find_if_not(_InputIterator, _InputIterator, _Predicate) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if_not(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/12/bits/stl_algo.h:516:32, inlined from 'bool std::all_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/12/bits/stl_algo.h:456:40, inlined from 'bool gemmi::Selection::matches(const gemmi::Atom&) const' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:199:23, inlined from 'bool gemmi::FilterIterPolicy::matches(std::size_t) const [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:187:62, inlined from 'void gemmi::FilterIterPolicy::increment() [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:188:62, inlined from 'gemmi::BidirIterator& gemmi::BidirIterator::operator++() [with Policy = gemmi::FilterIterPolicy, gemmi::Atom>]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:33:50, inlined from 'int residues_main(int, char**)' at /build/gemmi-0.5.7+ds/src/residues.cpp:169:50: /usr/include/c++/12/bits/stl_algo.h:109:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 109 | return std::__find_if(__first, __last, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 110 | __gnu_cxx::__ops::__negate(__pred), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/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++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; _Tp = gemmi::Restraints::Bond]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; _Tp = gemmi::Restraints::Angle]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; _Tp = gemmi::Restraints::Torsion]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; _Tp = gemmi::Restraints::Plane]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object CMakeFiles/program.dir/src/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/sf2map.cpp.o -MF CMakeFiles/program.dir/src/sf2map.cpp.o.d -o CMakeFiles/program.dir/src/sf2map.cpp.o -c /build/gemmi-0.5.7+ds/src/sf2map.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:16, from /build/gemmi-0.5.7+ds/src/sf2map.cpp:8: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; _Tp = gemmi::Restraints::Bond]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; _Tp = gemmi::Restraints::Angle]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; _Tp = gemmi::Restraints::Torsion]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; _Tp = gemmi::Restraints::Plane]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/model.hpp:15, from /build/gemmi-0.5.7+ds/src/rmsz.cpp:7: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Angle&}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'std::unique_ptr gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:424:20: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'std::unique_ptr gemmi::prepare_topology(Structure&, MonLib&, size_t, HydrogenChange, bool, std::ostream*, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/placeh.hpp:424:20: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::get_plane(const std::string&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::get_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:245:24, inlined from 'gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:250:48: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:253:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/gemmi-0.5.7+ds/include/gemmi/ccp4.hpp:9, from /build/gemmi-0.5.7+ds/src/sf2map.cpp:6: /usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_negate >]': /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Torsion&}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/ccp4.hpp:16: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::impl::parse_cid(const std::string&, gemmi::Selection&)' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:513:38: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Bond&}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/algorithm:61, from /build/gemmi-0.5.7+ds/include/gemmi/symmetry.hpp:15, from /build/gemmi-0.5.7+ds/include/gemmi/ccp4.hpp:17: In function '_InputIterator std::__find_if_not(_InputIterator, _InputIterator, _Predicate) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if_not(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/12/bits/stl_algo.h:516:32, inlined from 'bool std::all_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/12/bits/stl_algo.h:456:40, inlined from 'bool gemmi::Selection::matches(const gemmi::Atom&) const' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:199:23, inlined from 'bool gemmi::FilterIterPolicy::matches(std::size_t) const [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:187:62, inlined from 'gemmi::FilterIterPolicy::FilterIterPolicy(const Filter*, Vector*, std::size_t) [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:184:44, inlined from 'gemmi::FilterProxy::iterator gemmi::FilterProxy::begin() [with Filter = gemmi::Selection; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:207:48, inlined from 'void {anonymous}::transform_sf_to_map(OptParser&)' at /build/gemmi-0.5.7+ds/src/sf2map.cpp:82:51: /usr/include/c++/12/bits/stl_algo.h:109:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 109 | return std::__find_if(__first, __last, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 110 | __gnu_cxx::__ops::__negate(__pred), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_InputIterator std::__find_if_not(_InputIterator, _InputIterator, _Predicate) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if_not(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/12/bits/stl_algo.h:516:32, inlined from 'bool std::all_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Selection::matches(const gemmi::Atom&) const::]' at /usr/include/c++/12/bits/stl_algo.h:456:40, inlined from 'bool gemmi::Selection::matches(const gemmi::Atom&) const' at /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:199:23, inlined from 'bool gemmi::FilterIterPolicy::matches(std::size_t) const [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:187:62, inlined from 'void gemmi::FilterIterPolicy::increment() [with Filter = gemmi::Selection; Vector = std::vector; Value = gemmi::Atom]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:188:62, inlined from 'gemmi::BidirIterator& gemmi::BidirIterator::operator++() [with Policy = gemmi::FilterIterPolicy, gemmi::Atom>]' at /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:33:50, inlined from 'void {anonymous}::transform_sf_to_map(OptParser&)' at /build/gemmi-0.5.7+ds/src/sf2map.cpp:82:51: /usr/include/c++/12/bits/stl_algo.h:109:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 109 | return std::__find_if(__first, __last, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 110 | __gnu_cxx::__ops::__negate(__pred), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:421:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:453:39: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]', inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:479:41: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::get_plane(const std::string&)::]' at /usr/include/c++/12/bits/stl_algo.h:3877:28, inlined from 'std::vector::iterator gemmi::Restraints::get_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:245:24, inlined from 'void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const' at /build/gemmi-0.5.7+ds/include/gemmi/monlib.hpp:535:40: /usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 2112 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object CMakeFiles/program.dir/src/sfcalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/sfcalc.cpp.o -MF CMakeFiles/program.dir/src/sfcalc.cpp.o.d -o CMakeFiles/program.dir/src/sfcalc.cpp.o -c /build/gemmi-0.5.7+ds/src/sfcalc.cpp In file included from /usr/include/c++/12/vector:63: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]': /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; _Tp = gemmi::Restraints::Bond]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; _Tp = gemmi::Restraints::Angle]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; _Tp = gemmi::Restraints::Torsion]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; _Tp = gemmi::Restraints::Plane]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, inlined from 'gemmi::Restraints::Restraints(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gemmi-0.5.7+ds/include/gemmi/smcif.hpp:12, from /build/gemmi-0.5.7+ds/src/sfcalc.cpp:20: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 90%] Building CXX object CMakeFiles/program.dir/src/sg.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/sg.cpp.o -MF CMakeFiles/program.dir/src/sg.cpp.o.d -o CMakeFiles/program.dir/src/sg.cpp.o -c /build/gemmi-0.5.7+ds/src/sg.cpp In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Bond*; _Tp = gemmi::Restraints::Bond]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Angle*; _Tp = gemmi::Restraints::Angle]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Torsion*; _Tp = gemmi::Restraints::Torsion]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; _Tp = gemmi::Restraints::Plane]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, inlined from 'gemmi::Restraints& gemmi::Restraints::operator=(const gemmi::Restraints&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:25:8, inlined from 'gemmi::ChemComp& gemmi::ChemComp::operator=(const gemmi::ChemComp&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:285:8, inlined from 'void gemmi::Topo::initialize_refmac_topology(gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)' at /build/gemmi-0.5.7+ds/include/gemmi/topo.hpp:433:27: /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/gemmi-0.5.7+ds/include/gemmi/it92.hpp:16, from /build/gemmi-0.5.7+ds/src/sfcalc.cpp:12: /build/gemmi-0.5.7+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 5; Real = double]': /build/gemmi-0.5.7+ds/include/gemmi/dencalc.hpp:19:54: required from 'double gemmi::determine_cutoff_radius(double, const PrecalExpSum&, double) [with PrecalExpSum = ExpSum<5, double>]' /build/gemmi-0.5.7+ds/include/gemmi/dencalc.hpp:130:35: required from 'double gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, double) const [with int N = 5; Table = gemmi::IT92; Real = float; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<4, 1, double>]' /build/gemmi-0.5.7+ds/include/gemmi/dencalc.hpp:140:38: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<4, 1, double>; Table = gemmi::IT92; Real = float]' /build/gemmi-0.5.7+ds/include/gemmi/dencalc.hpp:116:32: required from 'void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::IT92; Real = float]' /build/gemmi-0.5.7+ds/include/gemmi/dencalc.hpp:179:11: required from 'void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::IT92; Real = float]' /build/gemmi-0.5.7+ds/include/gemmi/dencalc.hpp:184:5: required from 'void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::IT92; Real = float]' /build/gemmi-0.5.7+ds/src/sfcalc.cpp:232:36: required from 'void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::IT92; Real = float]' /build/gemmi-0.5.7+ds/src/sfcalc.cpp:654:23: required from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::IT92]' /build/gemmi-0.5.7+ds/src/sfcalc.cpp:757:44: required from here /build/gemmi-0.5.7+ds/include/gemmi/formfact.hpp:28:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 28 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object CMakeFiles/program.dir/src/tags.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/tags.cpp.o -MF CMakeFiles/program.dir/src/tags.cpp.o.d -o CMakeFiles/program.dir/src/tags.cpp.o -c /build/gemmi-0.5.7+ds/src/tags.cpp [ 95%] Building CXX object CMakeFiles/program.dir/src/validate.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/validate.cpp.o -MF CMakeFiles/program.dir/src/validate.cpp.o.d -o CMakeFiles/program.dir/src/validate.cpp.o -c /build/gemmi-0.5.7+ds/src/validate.cpp In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/ccp4.hpp:16, from /build/gemmi-0.5.7+ds/src/sfcalc.cpp:7: /usr/include/c++/12/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const double*; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 739 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::SmallStructure::Site&}; _Tp = gemmi::SmallStructure::Site; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::SmallStructure::AtomType&}; _Tp = gemmi::SmallStructure::AtomType; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::SmallStructure::Site; _Alloc = std::allocator]', inlined from 'gemmi::SmallStructure gemmi::make_small_structure_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/smcif.hpp:75:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::SmallStructure::AtomType; _Alloc = std::allocator]', inlined from 'gemmi::SmallStructure gemmi::make_small_structure_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/smcif.hpp:107:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/tao/pegtl/parse_error.hpp:13, from /usr/include/tao/pegtl/normal.hpp:14, from /usr/include/tao/pegtl/parse.hpp:11, from /usr/include/tao/pegtl.hpp:9, from /build/gemmi-0.5.7+ds/include/gemmi/cif.hpp:13, from /build/gemmi-0.5.7+ds/src/validate.cpp:3: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double, double}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double, double}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from '{anonymous}::Validator2::Validator2(gemmi::cif::Block&, const std::map, std::__cxx11::basic_regex >&)' at /build/gemmi-0.5.7+ds/src/validate.cpp:523:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:127:37: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::C4322]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const gemmi::Miller&) [with Table = gemmi::C4322]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:127:37: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::IT92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const gemmi::Miller&) [with Table = gemmi::IT92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:127:37: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::IT92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const gemmi::Miller&) [with Table = gemmi::IT92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:127:37, inlined from 'void {anonymous}::print_structure_factors_sm(const gemmi::SmallStructure&, gemmi::StructureFactorCalculator
&, bool, double, bool, const RefFile&) [with Table = gemmi::IT92]' at /build/gemmi-0.5.7+ds/src/sfcalc.cpp:366:62: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_model(const gemmi::Model&, const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:98:37: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::C4322]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_model(const gemmi::Model&, const gemmi::Miller&) [with Table = gemmi::C4322]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:98:37: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::IT92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_model(const gemmi::Model&, const gemmi::Miller&) [with Table = gemmi::IT92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:98:37: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Scaling::Point}; _Tp = gemmi::Scaling::Point; _Alloc = std::allocator::Point>]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::Point, std::allocator::Point> >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Scaling::Point}; _Tp = gemmi::Scaling::Point; _Alloc = std::allocator::Point>]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Scaling::Point; _Alloc = std::allocator::Point>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Scaling::prepare_points(const gemmi::AsuData >&, const gemmi::AsuData >&, const gemmi::AsuData >&) [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:200:25: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator::Point*, std::vector::Point, std::allocator::Point> > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Building CXX object CMakeFiles/program.dir/src/validate_mon.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/validate_mon.cpp.o -MF CMakeFiles/program.dir/src/validate_mon.cpp.o.d -o CMakeFiles/program.dir/src/validate_mon.cpp.o -c /build/gemmi-0.5.7+ds/src/validate_mon.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:110:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:113:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:115:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:119:19: /usr/include/c++/12/bits/stl_vector.h:1409:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1409 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1410 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:123:19: /usr/include/c++/12/bits/stl_vector.h:1409:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1409 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1410 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:127:19: /usr/include/c++/12/bits/stl_vector.h:1409:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1409 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1410 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:130:19: /usr/include/c++/12/bits/stl_vector.h:1409:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1409 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1410 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:133:19: /usr/include/c++/12/bits/stl_vector.h:1409:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1409 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1410 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:136:19: /usr/include/c++/12/bits/stl_vector.h:1409:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1409 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1410 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector gemmi::Scaling::get_parameters() const [with Real = float]' at /build/gemmi-0.5.7+ds/include/gemmi/scaling.hpp:139:22: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/cifdoc.hpp:8, from /build/gemmi-0.5.7+ds/src/validate_mon.cpp:8: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::C4322]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const gemmi::Miller&) [with Table = gemmi::C4322]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:127:37, inlined from 'void {anonymous}::print_structure_factors_sm(const gemmi::SmallStructure&, gemmi::StructureFactorCalculator
&, bool, double, bool, const RefFile&) [with Table = gemmi::C4322]' at /build/gemmi-0.5.7+ds/src/sfcalc.cpp:366:62, inlined from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::C4322]' at /build/gemmi-0.5.7+ds/src/sfcalc.cpp:661:33: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:487:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:494:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:502:29: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:253:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/chemcomp.hpp:535:54: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:35:31, inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/gemmi-0.5.7+ds/include/gemmi/sfcalc.hpp:127:37, inlined from 'void {anonymous}::print_structure_factors_sm(const gemmi::SmallStructure&, gemmi::StructureFactorCalculator
&, bool, double, bool, const RefFile&) [with Table = gemmi::Neutron92]' at /build/gemmi-0.5.7+ds/src/sfcalc.cpp:366:62, inlined from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::Neutron92]' at /build/gemmi-0.5.7+ds/src/sfcalc.cpp:661:33: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 97%] Building CXX object CMakeFiles/program.dir/src/wcn.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/wcn.cpp.o -MF CMakeFiles/program.dir/src/wcn.cpp.o.d -o CMakeFiles/program.dir/src/wcn.cpp.o -c /build/gemmi-0.5.7+ds/src/wcn.cpp In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:9, from /build/gemmi-0.5.7+ds/src/wcn.cpp:5: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:367:20, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:183:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:197:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from '{anonymous}::Result {anonymous}::test_bfactor_models(gemmi::Structure&, const Params&)' at /build/gemmi-0.5.7+ds/src/wcn.cpp:236:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from '{anonymous}::Result {anonymous}::test_bfactor_models(gemmi::Structure&, const Params&)' at /build/gemmi-0.5.7+ds/src/wcn.cpp:237:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [100%] Linking CXX executable gemmi /usr/bin/cmake -E cmake_link_script CMakeFiles/program.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/program.dir/src/align.cpp.o CMakeFiles/program.dir/src/blobs.cpp.o CMakeFiles/program.dir/src/cif2mtz.cpp.o CMakeFiles/program.dir/src/cif2json.cpp.o CMakeFiles/program.dir/src/contact.cpp.o CMakeFiles/program.dir/src/contents.cpp.o CMakeFiles/program.dir/src/convert.cpp.o CMakeFiles/program.dir/src/fprime.cpp.o CMakeFiles/program.dir/src/grep.cpp.o CMakeFiles/program.dir/src/h.cpp.o CMakeFiles/program.dir/src/json2cif.cpp.o CMakeFiles/program.dir/src/main.cpp.o CMakeFiles/program.dir/src/map.cpp.o CMakeFiles/program.dir/src/map2sf.cpp.o CMakeFiles/program.dir/src/mask.cpp.o CMakeFiles/program.dir/src/merge.cpp.o CMakeFiles/program.dir/src/mondiff.cpp.o CMakeFiles/program.dir/src/mtz.cpp.o CMakeFiles/program.dir/src/mtz2cif.cpp.o CMakeFiles/program.dir/src/prep.cpp.o CMakeFiles/program.dir/src/reindex.cpp.o CMakeFiles/program.dir/src/residues.cpp.o CMakeFiles/program.dir/src/rmsz.cpp.o CMakeFiles/program.dir/src/sf2map.cpp.o CMakeFiles/program.dir/src/sfcalc.cpp.o CMakeFiles/program.dir/src/sg.cpp.o CMakeFiles/program.dir/src/tags.cpp.o CMakeFiles/program.dir/src/validate.cpp.o CMakeFiles/program.dir/src/validate_mon.cpp.o CMakeFiles/program.dir/src/wcn.cpp.o CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o CMakeFiles/input.dir/src/input.cpp.o CMakeFiles/output.dir/src/output.cpp.o CMakeFiles/options.dir/src/options.cpp.o -o gemmi /usr/lib/arm-linux-gnueabihf/libz.so make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [100%] Built target program /usr/include/pybind11/pybind11.h: In member function 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-MD -MT CMakeFiles/cpptest.dir/tests/main.cpp.o -MF CMakeFiles/cpptest.dir/tests/main.cpp.o.d -o CMakeFiles/cpptest.dir/tests/main.cpp.o -c /build/gemmi-0.5.7+ds/tests/main.cpp In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/util.hpp:13, from /build/gemmi-0.5.7+ds/include/gemmi/fileutil.hpp:16, from /build/gemmi-0.5.7+ds/include/gemmi/gz.hpp:14, from /build/gemmi-0.5.7+ds/examples/check_conn.cpp:5: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:358:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:360:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:9, from /build/gemmi-0.5.7+ds/tests/disulf.cpp:8: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:358:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:360:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:284:27: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:292:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:335:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'void gemmi::impl::read_connectivity(gemmi::cif::Block&, gemmi::Structure&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:240:32: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:367:20, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/gemmi-0.5.7+ds/include/gemmi/neighbor.hpp:183:61: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:503:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:518:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:524:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:535:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::NcsOp; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:629:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:769:31: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::impl::apply_hd_mixture(gemmi::Residue*, double)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:448:24, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:771:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/doctest/doctest.h:3125, from /build/gemmi-0.5.7+ds/tests/main.cpp:3: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::ostream* doctest::detail::::push()' at /usr/include/doctest/doctest.h:3290:28, inlined from 'std::ostream* doctest::detail::tlssPush()' at /usr/include/doctest/doctest.h:3307:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:335:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/gemmi-0.5.7+ds/include/gemmi/iterator.hpp:10, from /build/gemmi-0.5.7+ds/include/gemmi/cifdoc.hpp:8, from /build/gemmi-0.5.7+ds/include/gemmi/chemcomp_xyz.hpp:9, from /build/gemmi-0.5.7+ds/include/gemmi/mmread.hpp:8, from /build/gemmi-0.5.7+ds/docs/code/maybegz.cpp:2: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:358:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:360:30: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF CMakeFiles/cpptest.dir/tests/cif.cpp.o.d -o CMakeFiles/cpptest.dir/tests/cif.cpp.o -c /build/gemmi-0.5.7+ds/tests/cif.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:1176, from /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:15, from /build/gemmi-0.5.7+ds/tests/cif.cpp:93: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:503:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:518:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:524:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:535:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::impl::apply_hd_mixture(gemmi::Residue*, double)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:448:24, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:771:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 31%] Linking CXX executable check_conn /usr/bin/cmake -E cmake_link_script CMakeFiles/check_conn.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn /usr/lib/arm-linux-gnueabihf/libz.so In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', inlined from 'std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:335:36: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 31%] Built target check_conn make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' cd /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/hello.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 34%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/hello.dir/examples/hello.cpp.o -MF CMakeFiles/hello.dir/examples/hello.cpp.o.d -o CMakeFiles/hello.dir/examples/hello.cpp.o -c /build/gemmi-0.5.7+ds/examples/hello.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:503:36: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:518:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:524:34: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:535:39: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::impl::apply_hd_mixture(gemmi::Residue*, double)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:448:24, inlined from 'gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)' at /build/gemmi-0.5.7+ds/include/gemmi/mmcif.hpp:771:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 34%] Linking CXX executable hello /usr/bin/cmake -E cmake_link_script CMakeFiles/hello.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/hello.dir/examples/hello.cpp.o -o hello [ 36%] Linking CXX executable test_disulf /usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf /usr/lib/arm-linux-gnueabihf/libz.so make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 36%] Built target hello make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' cd /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/doc_newmtz.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 36%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/newmtz.cpp [ 36%] Built target test_disulf make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' cd /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/DependInfo.cmake --color= Dependencies file "CMakeFiles/program.dir/src/align.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". 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Dependencies file "CMakeFiles/program.dir/src/main.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/map.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/map2sf.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/mask.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/merge.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". 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Dependencies file "CMakeFiles/program.dir/src/residues.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/rmsz.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/sf2map.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/sfcalc.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/sg.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/tags.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/validate.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/validate_mon.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". Dependencies file "CMakeFiles/program.dir/src/wcn.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/compiler_depend.internal". In file included from /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:1176, from /build/gemmi-0.5.7+ds/docs/code/newmtz.cpp:2: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. 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[with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/gemmi-0.5.7+ds/include/gemmi/unitcell.hpp:348:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void gemmi::Mtz::add_base()' at /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:221:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'gemmi::Mtz::Dataset& gemmi::Mtz::add_dataset(const std::string&)' at /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:930:23, inlined from 'int main()' at /build/gemmi-0.5.7+ds/docs/code/newmtz.cpp:10:18: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable doc_newmtz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [100%] Built target doc_newmtz make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' cd /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/check.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' /usr/bin/ctest -C None Test project /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf Start 1: cpptest 1/1 Test #1: cpptest .......................... Passed 0.01 sec 100% tests passed, 0 tests failed out of 1 Total Test time (real) = 0.01 sec make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [100%] Built target check make[4]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles 0 make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make[2]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' PYTHONPATH=$(find . -name 'obj-*') pytest-3 -k 'not test_sfcalc_' ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/gemmi-0.5.7+ds collected 173 items / 2 deselected / 171 selected tests/test_align.py ... [ 1%] tests/test_cif.py ..................... [ 14%] tests/test_cif_json.py ..... [ 16%] tests/test_elem.py ..... [ 19%] tests/test_examples.py ............ [ 26%] tests/test_grid.py ...... [ 30%] tests/test_hkl.py ....... [ 34%] tests/test_misc.py .. [ 35%] tests/test_mol.py ........................................... [ 60%] tests/test_monlib.py ........ [ 65%] tests/test_neighbor.py ..... [ 68%] tests/test_prog.py sssssssss [ 73%] tests/test_sf.py . [ 74%] tests/test_smallmol.py .... [ 76%] tests/test_symmetry.py ...................... [ 89%] tests/test_twin.py .... [ 91%] tests/test_unitcell.py .............. [100%] ================= 162 passed, 9 skipped, 2 deselected in 4.31s ================= make[1]: Leaving directory '/build/gemmi-0.5.7+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/gemmi-0.5.7\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/gemmi-0.5.7+ds -B/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/bin/gemmi -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/symmetry.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/model.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/binner.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/topo.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/fileutil.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/small.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/contact.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/to_json.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/cellred.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/reciproc.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/json.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/metadata.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/cifdoc.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/atof.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/solmask.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/third_party -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/third_party/tinydir.h -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/third_party/sajson.h -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/resinfo.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/polyheur.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/mtz.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/merge.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/numb.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/it92.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/elem.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/seqalign.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/neutron92.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/fprime.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/read_cif.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/qcp.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/math.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/seqid.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/asudata.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/align.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/atox.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/floodfill.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/ccp4.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/asumask.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/reindex.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/pdb.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/c4322.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/to_mmdb.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/refln.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/scaling.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/select.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/levmar.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/input.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/fourier.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/grid.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/monlib.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/crd.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/dirwalk.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/util.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/read_map.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/smcif.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/sprintf.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/to_cif.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/remarks.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/eig3.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/fstream.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/addends.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/span.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/cif.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/interop.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/bessel.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/formfact.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/twin.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/dencalc.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/modify.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/to_pdb.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/unitcell.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/placeh.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/fail.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/enumstr.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/gz.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/mmcif.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/assembly.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/read_coor.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/sfcalc.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/utf.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/cif2mtz.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/version.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/iterator.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/blob.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/calculate.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/mmread.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/recgrid.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/include/gemmi/neighbor.hpp -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi.cpython-311-arm-linux-gnueabihf.so -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/rama_plot.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/mtz_i_sigi.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/maskdiff.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/long_geom.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/rama_gather.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/monomers.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/sub_ccd.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/map2mtz.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/simple_search.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/patterson_slice.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/weight.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/aafreq.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/ccd_gi.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/ccd_subgraph.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/mtrix_iso.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/multiproc.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/merge_mtz_mmcif.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/__main__.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/cif_i_sigi.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/col_order.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/__init__.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/__pycache__ -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/from_json.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/hello.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/maskcheck.py -- Installing: /build/gemmi-0.5.7+ds/debian/tmp/usr/local/lib/python3.11/dist-packages/gemmi-examples/matthews.py make[1]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake debian/rules override_dh_installman make[1]: Entering directory '/build/gemmi-0.5.7+ds' help2man 'tail -n +9 docs/gemmi-help.txt' \ --version-string 0.5.7+ds --name 'CLI for GEMMI library' \ --no-info --help-option '' > debian/gemmi.1 sed -i 's/.TH GEMMI-HELP.TXT/.TH gemmi/' debian/gemmi.1 sed -i 's/gemmi-help.txt/gemmi/' debian/gemmi.1 dh_installman make[1]: Leaving directory '/build/gemmi-0.5.7+ds' dh_python3 -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/python3-gemmi/usr/lib/python3/dist-packages/gemmi.cpython-311-arm-linux-gnueabihf.so: .debug_info section not present dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: debian/gemmi/usr/bin/gemmi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Provides field of package python3-gemmi: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.5.7+ds-2_armhf.deb'. dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.5.7+ds-2_armhf.deb'. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.5.7+ds-2_armhf.deb'. dpkg-deb: building package 'gemmi' in '../gemmi_0.5.7+ds-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.5.7+ds-2_armhf.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.5.7+ds-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/25145/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/25145/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/25145 and its subdirectories I: Current time: Sun Jun 4 02:32:30 +14 2023 I: pbuilder-time-stamp: 1685795550