Diff of the two buildlogs: -- --- b1/build.log 2023-06-03 11:46:46.015108334 +0000 +++ b2/build.log 2023-06-03 12:32:35.454714767 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jun 2 18:43:30 -12 2023 -I: pbuilder-time-stamp: 1685774610 +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 @@ -16,7 +16,7 @@ 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 Mon Oct 3 20:32:52 2022 -12 +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 @@ -30,135 +30,167 @@ 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/24213/tmp/hooks/D02_print_environment starting +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 - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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='3f5b07f765c941e19e6ad06de7e43b68' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='24213' - PS1='# ' - PS2='> ' + 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' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2hMiqwe5/pbuilderrc_23Sy --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2hMiqwe5/b1 --logfile b1/build.log gemmi_0.5.7+ds-2.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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 wbq0 5.10.0-23-armmp #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux + 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 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/24213/tmp/hooks/D02_print_environment finished + -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 @@ -307,7 +339,7 @@ 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 9s (5193 kB/s) +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.) @@ -689,8 +721,19 @@ 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: Running cd /build/gemmi-0.5.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gemmi_0.5.7+ds-2_source.changes +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 @@ -750,50 +793,48 @@ -- 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 -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + 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 -f CMakeFiles/options.dir/build.make CMakeFiles/options.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/input.dir/DependInfo.cmake --color= -make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/depend +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.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/options.dir/DependInfo.cmake --color= +make -f CMakeFiles/output.dir/build.make CMakeFiles/output.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/output.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +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 -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build -make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' 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 directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 2%] 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 +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build +make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build +make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +[ 2%] Building CXX object CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o [ 4%] Building CXX object CMakeFiles/input.dir/src/input.cpp.o -[ 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/mapcoef.dir/src/mapcoef.cpp.o -MF CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o.d -o 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." | ^~~~~~~ -make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 4%] Built target options -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/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build -make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 7%] Building CXX object CMakeFiles/mapcoef.dir/src/mapcoef.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/mapcoef.dir/src/mapcoef.cpp.o -MF CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o.d -o CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o -c /build/gemmi-0.5.7+ds/src/mapcoef.cpp 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 >]': @@ -801,6 +842,21 @@ 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, @@ -824,6 +880,14 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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, @@ -867,16 +931,8 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::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::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 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 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 = {}; _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]': @@ -933,19 +989,12 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 7%] Built target mapcoef -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= +[ 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' -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." - | ^~~~~~~ +[ 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 @@ -972,22 +1021,27 @@ /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' -[ 7%] Built target output -[ 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 -[ 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 -make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 12%] Built target input +[ 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' -[ 12%] Building CXX object CMakeFiles/program.dir/src/align.cpp.o +[ 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: @@ -995,8 +1049,8 @@ /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>:: | ^~~~~~~~~~~~~~~~~~~ -[ 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 +[ 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: @@ -1018,8 +1072,10 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 17%] Building CXX object CMakeFiles/program.dir/src/blobs.cpp.o +[ 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: @@ -1074,14 +1130,14 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] 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 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: @@ -1126,8 +1182,12 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] 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 +[ 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, @@ -1153,8 +1213,6 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] 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 /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>:: @@ -1164,10 +1222,18 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] 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: +[ 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." | ^~~~~~~ @@ -1210,13 +1276,17 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 24%] Building CXX object CMakeFiles/program.dir/src/contents.cpp.o +[ 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, @@ -1240,13 +1310,29 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object CMakeFiles/program.dir/src/convert.cpp.o +[ 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, @@ -1329,6 +1415,13 @@ /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>:: @@ -1372,6 +1465,8 @@ /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: @@ -1412,6 +1507,12 @@ /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 @@ -1426,9 +1527,7 @@ /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)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] 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 -[ 29%] Building CXX object CMakeFiles/program.dir/src/fprime.cpp.o +[ 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, @@ -1449,14 +1548,19 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 31%] Building CXX object CMakeFiles/program.dir/src/grep.cpp.o +[ 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 -[ 34%] 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 -[ 36%] Building CXX object CMakeFiles/program.dir/src/h.cpp.o +[ 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 -[ 36%] 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 +[ 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, @@ -1497,10 +1601,10 @@ /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, | ^~~~~~~~~~~~~ -[ 39%] 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 -[ 41%] 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 +[ 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>:: @@ -1614,11 +1718,43 @@ /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 @@ -1662,10 +1798,38 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] 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 -[ 46%] 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 +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 @@ -1686,6 +1850,11 @@ /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 @@ -1723,6 +1892,12 @@ /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, @@ -1760,10 +1935,34 @@ /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); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] 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 -[ 48%] 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 +/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, @@ -1808,6 +2007,41 @@ /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, @@ -1844,6 +2078,14 @@ /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, @@ -1866,160 +2108,6 @@ /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)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 51%] 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 -[ 51%] 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 -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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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::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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 51%] 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 -[ 53%] 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 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)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 56%] 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 -/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>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 58%] 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 -/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 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 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: @@ -2042,6 +2130,8 @@ /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, @@ -2066,6 +2156,16 @@ /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: @@ -2074,14 +2174,50 @@ 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 = {}; _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 +/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>:: | ^~~~~~~~~~~~~~~~~~~ -/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 +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 @@ -2092,6 +2228,30 @@ /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]': @@ -2167,92 +2327,20 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] 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 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); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 63%] 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 -[ 63%] Building CXX object CMakeFiles/program.dir/src/mtz2cif.cpp.o +[ 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." | ^~~~~~~ -[ 63%] 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 +[ 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, @@ -2284,13 +2372,8 @@ /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)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] 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." - | ^~~~~~~ +[ 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>:: @@ -2341,6 +2424,18 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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, @@ -2366,6 +2461,26 @@ /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 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: @@ -2421,38 +2536,26 @@ /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 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 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 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, @@ -2510,18 +2613,22 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 68%] 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 +/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 -[ 70%] 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 /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: @@ -2534,6 +2641,8 @@ /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 @@ -2543,6 +2652,11 @@ /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: @@ -2598,12 +2712,12 @@ /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>:: | ^~~~~~~~~~~~~~~~~~~ -[ 73%] 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 = {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]', @@ -2625,6 +2739,13 @@ /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 @@ -2650,31 +2771,16 @@ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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 + 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>:: | ^~~~~~~~~~~~~~~~~~~ -/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 +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: @@ -2683,16 +2789,56 @@ 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 -[ 75%] 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 /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 -[ 75%] 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 /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, @@ -2738,6 +2884,13 @@ /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, @@ -2782,16 +2935,13 @@ /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/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/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: @@ -2812,95 +2962,6 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] 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 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." - | ^~~~~~~ -[ 78%] 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 -[ 80%] 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." - | ^~~~~~~ -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 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/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)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] 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 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>:: - | ^~~~~~~~~~~~~~~~~~~ /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 >]', @@ -2942,12 +3003,66 @@ /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: @@ -2973,6 +3088,8 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 @@ -3020,6 +3137,13 @@ /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, @@ -3064,29 +3188,6 @@ /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); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] 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." - | ^~~~~~~ -[ 87%] 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 /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." - | ^~~~~~~ -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 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]': @@ -3102,57 +3203,10 @@ /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/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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] 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." - | ^~~~~~~ +[ 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: @@ -3182,8 +3236,6 @@ /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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] 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 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: @@ -3195,6 +3247,22 @@ /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 /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>:: @@ -3250,9 +3318,6 @@ /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); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 90%] 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 /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>:: @@ -3263,6 +3328,8 @@ /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>:: @@ -3329,46 +3396,6 @@ /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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 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 -lto-wrapper: warning: using serial compilation of 112 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information -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); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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 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); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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 -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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -3383,6 +3410,14 @@ /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: @@ -3408,6 +3443,14 @@ /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 '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, @@ -3469,7 +3512,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/gemmi-0.5.7+ds' dh_auto_build -- check - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" check VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" check VERBOSE=1 make[2]: 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 check @@ -3478,92 +3521,114 @@ /usr/bin/cmake -E cmake_progress_start /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles 41 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/depend -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.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_conn.dir/DependInfo.cmake --color= +make -f CMakeFiles/input.dir/build.make CMakeFiles/input.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/output.dir/DependInfo.cmake --color= 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/options.dir/DependInfo.cmake --color= -Dependencies file "CMakeFiles/options.dir/src/options.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/options.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build -Consolidate compiler generated dependencies of target options -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build -Dependencies file "CMakeFiles/output.dir/src/output.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/output.dir/compiler_depend.internal". +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/test_disulf.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -Consolidate compiler generated dependencies of target output +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/input.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -make[5]: Nothing to be done for 'CMakeFiles/options.dir/build'. +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_conn.dir/DependInfo.cmake --color= +Dependencies file "CMakeFiles/output.dir/src/output.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/output.dir/compiler_depend.internal". make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +Dependencies file "CMakeFiles/input.dir/src/input.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/input.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target output make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/build +Consolidate compiler generated dependencies of target input +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build +[ 2%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.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/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /build/gemmi-0.5.7+ds/tests/disulf.cpp +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build +make[5]: Entering 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' make[5]: Nothing to be done for 'CMakeFiles/output.dir/build'. make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 2%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make[5]: Nothing to be done for 'CMakeFiles/input.dir/build'. +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +[ 7%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o +[ 7%] Built target output +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend /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/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/gemmi-0.5.7+ds/examples/check_conn.cpp -[ 2%] Built target options +[ 9%] Built target input make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.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/options.dir/DependInfo.cmake --color= +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/mapcoef.dir/DependInfo.cmake --color= +Dependencies file "CMakeFiles/options.dir/src/options.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/options.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target options +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +make[5]: Nothing to be done for 'CMakeFiles/options.dir/build'. +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' Dependencies file "CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/mapcoef.dir/compiler_depend.internal". -[ 4%] Built target output -make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/depend Consolidate compiler generated dependencies of target mapcoef make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build 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/input.dir/DependInfo.cmake --color= -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make[5]: Nothing to be done for 'CMakeFiles/mapcoef.dir/build'. make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 7%] Built target mapcoef +[ 9%] Built target options +make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.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/doc_example.dir/DependInfo.cmake --color= +[ 12%] Built target mapcoef make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/depend -Dependencies file "CMakeFiles/input.dir/src/input.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/CMakeFiles/input.dir/compiler_depend.internal". 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_example2.dir/DependInfo.cmake --color= -Consolidate compiler generated dependencies of target input make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build +make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -make[5]: Nothing to be done for 'CMakeFiles/input.dir/build'. -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 9%] Built target input +[ 14%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.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 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/sym.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/sym.cpp +[ 17%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.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_example2.dir/docs/code/cif_cc.cpp.o -MF CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o.d -o CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/cif_cc.cpp +[ 19%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.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 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/elem.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/elem.cpp +[ 21%] Building CXX object CMakeFiles/doc_example.dir/docs/code/resinfo.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 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/resinfo.cpp +[ 21%] Building CXX object CMakeFiles/doc_example.dir/docs/code/cell.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 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/cell.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/cell.cpp +[ 24%] Linking CXX executable doc_example +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example.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_example.dir/docs/code/sym.cpp.o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -o doc_example +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +[ 24%] Built target doc_example make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.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/doc_maybegz.dir/DependInfo.cmake --color= -[ 12%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.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_example2.dir/docs/code/cif_cc.cpp.o -MF CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o.d -o CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/cif_cc.cpp make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 14%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o +[ 26%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.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_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/maybegz.cpp -[ 14%] Linking CXX executable doc_example2 +[ 26%] Linking CXX executable doc_example2 /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.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_example2.dir/docs/code/cif_cc.cpp.o -o doc_example2 make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 14%] Built target doc_example2 -make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend +[ 26%] Built target doc_example2 +make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.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/doc_newmtz.dir/DependInfo.cmake --color= +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/cpptest.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 -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 14%] 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 -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. It may not work." - | ^~~~~~~ +[ 29%] Building CXX object CMakeFiles/cpptest.dir/tests/main.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/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, @@ -3603,12 +3668,17 @@ /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/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: + 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>:: @@ -3625,26 +3695,41 @@ /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: 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 -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::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::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)...); @@ -3671,45 +3756,165 @@ /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 -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 +/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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 +/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::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 +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::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]': +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 '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 +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 /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:17: -/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]': + 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>:: | ^~~~~~~~~~~~~~~~~~~ -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: 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>:: @@ -3720,10 +3925,6 @@ /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 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>:: @@ -3736,36 +3937,6 @@ /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 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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] 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' -[ 17%] Built target doc_newmtz -make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.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/cpptest.dir/DependInfo.cmake --color= -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 19%] Building CXX object CMakeFiles/cpptest.dir/tests/main.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/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 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 @@ -3786,43 +3957,35 @@ /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 = {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: 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 '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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 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); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 @@ -3849,66 +4012,24 @@ /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/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." - | ^~~~~~~ -[ 21%] 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 -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 21%] 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' -[ 24%] 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 -[ 26%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.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_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/mutate.cpp -[ 26%] Linking CXX executable hello +[ 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' -[ 26%] Built target hello -make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.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/doc_example.dir/DependInfo.cmake --color= -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/build -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.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 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/sym.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/sym.cpp -[ 31%] Linking CXX executable doc_maybegz -/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.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_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz /usr/lib/arm-linux-gnueabihf/libz.so +[ 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' -[ 31%] Built target doc_maybegz -make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.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/test_disulf.dir/DependInfo.cmake --color= +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/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build +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' -[ 34%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.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/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /build/gemmi-0.5.7+ds/tests/disulf.cpp -[ 36%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.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 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/elem.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/elem.cpp -[ 39%] Building CXX object CMakeFiles/doc_example.dir/docs/code/resinfo.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 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/resinfo.cpp -[ 39%] Building CXX object CMakeFiles/doc_example.dir/docs/code/cell.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 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/cell.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/cell.cpp -[ 41%] Linking CXX executable doc_example -/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example.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_example.dir/docs/code/sym.cpp.o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -o doc_example -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 41%] Built target doc_example +[ 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= @@ -3942,153 +4063,75 @@ 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. It may not work." + | ^~~~~~~ Consolidate compiler generated dependencies of target program make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make[5]: Nothing to be done for 'CMakeFiles/program.dir/build'. make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 95%] Built target program +[ 90%] Built target program make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.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/print-version.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 97%] gemmi --version +[ 92%] gemmi --version cd /build/gemmi-0.5.7+ds && /build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf/gemmi --version gemmi 0.5.7 make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' -[ 97%] Built target print-version +[ 92%] Built target print-version +[ 95%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.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_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/mutate.cpp +[ 97%] Linking CXX executable doc_maybegz +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 [ 97%] Linking CXX executable cpptest /usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.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_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz /usr/lib/arm-linux-gnueabihf/libz.so /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/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o -o cpptest make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' [ 97%] Built target cpptest +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-arm-linux-gnueabihf' +[ 97%] Built target doc_maybegz 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 -/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)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + from /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:17: /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]': +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: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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/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 +/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::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::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 = {}; _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 +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 = {}; _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 +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)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[100%] 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 +[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 test_disulf +[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= @@ -4098,11 +4141,11 @@ /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 0.07 sec +1/1 Test #1: cpptest .......................... Passed 0.01 sec 100% tests passed, 0 tests failed out of 1 -Total Test time (real) = 0.15 sec +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' @@ -4133,13 +4176,13 @@ tests/test_twin.py .... [ 91%] tests/test_unitcell.py .............. [100%] -================ 162 passed, 9 skipped, 2 deselected in 28.50s ================= +================= 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 -j3 install DESTDIR=/build/gemmi-0.5.7\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + 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 @@ -4151,132 +4194,132 @@ -- 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/mmcif_impl.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/neighbor.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/mmread.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/it92.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/addends.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/math.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/align.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/polyheur.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/chemcomp_xyz.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/neutron92.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/ccp4.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/atox.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/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/cif.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/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/read_coor.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/levmar.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/iterator.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/binner.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/read_map.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/to_chemcomp.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/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/unitcell.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/bessel.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/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/resinfo.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/to_json.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/atof.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/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/symmetry.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/version.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/utf.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/formfact.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/c4322.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/pdb.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/select.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/asudata.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/xds_ascii.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/assembly.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/numb.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/fileutil.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/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/scaling.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/cifdoc.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/to_cif.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/dirwalk.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/metadata.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/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/tinydir.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/linkhunt.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/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/col_order.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/aafreq.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/mtz_i_sigi.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/ccd_subgraph.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/monomers.py -- 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/sub_ccd.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/__init__.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/from_json.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/simple_search.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/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 @@ -4310,10 +4353,10 @@ 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 'gemmi' in '../gemmi_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-dbgsym' in '../gemmi-dbgsym_0.5.7+ds-2_armhf.deb'. 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) @@ -4321,12 +4364,14 @@ 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/24213 and its subdirectories -I: Current time: Fri Jun 2 23:46:40 -12 2023 -I: pbuilder-time-stamp: 1685792800 +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