https://launchpad.net/ubuntu/+archive/test-rebuild-20211217-jammy-gcc12/+build/22765110 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-071 4.15.0-166-generic #174-Ubuntu SMP Wed Dec 8 19:08:37 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_206~519~ubuntu18.04.1 python3-lpbuildd_206~519~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 15 Jan 00:11:20 ntpdate[1683]: adjust time server 10.211.37.1 offset -0.012373 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22765110 --image-type chroot /home/buildd/filecache-default/c698bf6badd89264039f6cdfcd7c983f87611a3e Creating target for build PACKAGEBUILD-22765110 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22765110 Starting target for build PACKAGEBUILD-22765110 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22765110 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu jammy main' 'deb http://ftpmaster.internal/ubuntu jammy main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-22765110 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22765110 Adding trusted keys to build-PACKAGEBUILD-22765110 Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). OK Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22765110 Updating target for build PACKAGEBUILD-22765110 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy InRelease [23.8 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu jammy InRelease [23.8 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main armhf Packages [7892 B] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main Translation-en [7676 B] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf Packages [1352 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu jammy/main armhf Packages [3872 B] Get:8 http://ftpmaster.internal/ubuntu jammy/main Translation-en [519 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu jammy/main Translation-en [5972 B] Get:10 http://ftpmaster.internal/ubuntu jammy/restricted armhf Packages [10.2 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/restricted Translation-en [13.3 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/universe armhf Packages [13.3 MB] Get:13 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5584 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/multiverse armhf Packages [168 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/multiverse Translation-en [111 kB] Fetched 21.4 MB in 5s (4400 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libssl1.1 Use 'sudo apt autoremove' to remove it. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: gcc-12-base libexpat1 libmpdec3 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libsemanage2 libsepol2 libssl3 media-types python3 python3-minimal python3-psutil python3.9 python3.9-minimal The following packages have been kept back: cpp g++ gcc The following packages will be upgraded: apt base-files bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils bzip2 ca-certificates cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libbz2-1.0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdpkg-perl libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 lockfile-progs login logsave lto-disabled-list make mount ncurses-base ncurses-bin openssl passwd pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv systemd-timesyncd tzdata usrmerge util-linux 105 upgraded, 15 newly installed, 1 to remove and 3 not upgraded. Need to get 73.7 MB of archives. After this operation, 318 MB disk space will be freed. Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main armhf gcc-12-base armhf 12-20220106-1ubuntu1 [19.5 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf debconf all 1.5.79 [126 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main armhf libgcc-s1 armhf 12-20220106-1ubuntu1 [42.6 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main armhf libstdc++6 armhf 12-20220106-1ubuntu1 [583 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf libpam0g armhf 1.4.0-10ubuntu2 [56.0 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt-dev armhf 1:4.4.27-1 [122 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt1 armhf 1:4.4.27-1 [94.0 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf base-files armhf 12ubuntu2 [63.0 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf debianutils armhf 5.5-1ubuntu1 [106 kB] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu jammy/main armhf dpkg armhf 1.21.1ubuntu11 [1204 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main armhf bash armhf 5.1-6ubuntu1 [655 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main armhf bsdutils armhf 1:2.37.2-4ubuntu1 [86.9 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf libgpg-error0 armhf 1.43-1 [61.8 kB] Get:14 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main armhf libgomp1 armhf 12-20220106-1ubuntu1 [109 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf libgcrypt20 armhf 1.9.4-3ubuntu2 [438 kB] Get:16 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main armhf libatomic1 armhf 12-20220106-1ubuntu1 [7642 B] Get:17 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main armhf libubsan1 armhf 12-20220106-1ubuntu1 [958 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf bzip2 armhf 1.0.8-5 [34.2 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf libbz2-1.0 armhf 1.0.8-5 [31.7 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf libssl3 armhf 3.0.1-0ubuntu1 [1577 kB] Get:21 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu jammy/main armhf libcc1-0 armhf 12-20220106-1ubuntu1 [39.0 kB] Get:22 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu jammy/main armhf dpkg-dev all 1.21.1ubuntu11 [926 kB] Get:23 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu jammy/main armhf libdpkg-perl all 1.21.1ubuntu11 [236 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf libblkid1 armhf 2.37.2-4ubuntu1 [136 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf libuuid1 armhf 2.37.2-4ubuntu1 [23.3 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf libcryptsetup12 armhf 2:2.4.2-1ubuntu4 [186 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf libidn2-0 armhf 2.3.2-2 [67.8 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf libp11-kit0 armhf 0.24.0-6 [219 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf libtasn1-6 armhf 4.18.0-4 [36.3 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf libgnutls30 armhf 3.7.2-5ubuntu1 [922 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf systemd-sysv armhf 249.5-2ubuntu3 [10.5 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main armhf systemd-timesyncd armhf 249.5-2ubuntu3 [30.7 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main armhf libapparmor1 armhf 3.0.3-0ubuntu5 [32.4 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main armhf libip4tc2 armhf 1.8.7-1ubuntu4 [17.7 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main armhf libzstd1 armhf 1.4.8+dfsg-3 [285 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main armhf libkmod2 armhf 28-1ubuntu5 [40.9 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main armhf libpcre2-8-0 armhf 10.39-3 [190 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main armhf libselinux1 armhf 3.3-1 [66.9 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main armhf libmount1 armhf 2.37.2-4ubuntu1 [151 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main armhf libseccomp2 armhf 2.5.2-2ubuntu2 [47.7 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main armhf login armhf 1:4.8.1-2ubuntu1 [186 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main armhf util-linux armhf 2.37.2-4ubuntu1 [1130 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main armhf mount armhf 2.37.2-4ubuntu1 [125 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main armhf systemd armhf 249.5-2ubuntu3 [4440 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main armhf libsystemd0 armhf 249.5-2ubuntu3 [296 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main armhf libudev1 armhf 249.5-2ubuntu3 [70.6 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main armhf libapt-pkg6.0 armhf 2.3.14 [899 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main armhf dash armhf 0.5.11+git20210903+057cd650a4ed-3 [83.8 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main armhf grep armhf 3.7-1 [150 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main armhf libncurses6 armhf 6.3-1 [87.5 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main armhf libncursesw6 armhf 6.3-1 [118 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main armhf libtinfo6 armhf 6.3-1 [88.2 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-bin armhf 6.3-1 [175 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main armhf sed armhf 4.8-1ubuntu1 [186 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main armhf init-system-helpers all 1.61 [39.3 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-base all 6.3-1 [19.9 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main armhf gpgv armhf 2.2.27-3ubuntu1 [186 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main armhf apt armhf 2.3.14 [1379 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main armhf libsepol2 armhf 3.3-1 [263 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main armhf libsemanage-common all 3.3-1 [10.1 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main armhf libsemanage2 armhf 3.3-1 [84.0 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main armhf passwd armhf 1:4.8.1-2ubuntu1 [740 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules-bin armhf 1.4.0-10ubuntu2 [35.6 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules armhf 1.4.0-10ubuntu2 [263 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main armhf logsave armhf 1.46.5-2ubuntu1 [10.1 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main armhf libext2fs2 armhf 1.46.5-2ubuntu1 [191 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main armhf e2fsprogs armhf 1.46.5-2ubuntu1 [566 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main armhf init armhf 1.61 [6102 B] Get:69 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.9-minimal armhf 3.9.9-2 [776 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main armhf libexpat1 armhf 2.4.2-1 [64.9 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main armhf python3.9-minimal armhf 3.9.9-2 [1749 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main armhf python3-minimal armhf 3.9.7-4 [24.7 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main armhf media-types all 4.0.0 [22.2 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main armhf tzdata all 2021e-1ubuntu1 [343 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main armhf libmpdec3 armhf 2.5.1-2build1 [76.5 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main armhf readline-common all 8.1.2-1 [53.5 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main armhf libreadline8 armhf 8.1.2-1 [128 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main armhf libsqlite3-0 armhf 3.36.0-2 [571 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.9-stdlib armhf 3.9.9-2 [1731 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main armhf python3.9 armhf 3.9.9-2 [437 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3-stdlib armhf 3.9.7-4 [7298 B] Get:82 http://ftpmaster.internal/ubuntu jammy/main armhf python3 armhf 3.9.7-4 [22.8 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main armhf libattr1 armhf 1:2.5.1-1 [12.2 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main armhf libcom-err2 armhf 1.46.5-2ubuntu1 [9002 B] Get:85 http://ftpmaster.internal/ubuntu jammy/main armhf libk5crypto3 armhf 1.19.2-0ubuntu1 [83.6 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main armhf libkrb5support0 armhf 1.19.2-0ubuntu1 [30.5 kB] Get:87 http://ftpmaster.internal/ubuntu jammy/main armhf libkrb5-3 armhf 1.19.2-0ubuntu1 [330 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main armhf libgssapi-krb5-2 armhf 1.19.2-0ubuntu1 [120 kB] Get:89 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-runtime all 1.4.0-10ubuntu2 [40.2 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/main armhf libsmartcols1 armhf 2.37.2-4ubuntu1 [93.7 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main armhf libasan6 armhf 11.2.0-13ubuntu1 [2243 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main armhf g++-11 armhf 11.2.0-13ubuntu1 [9009 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11 armhf 11.2.0-13ubuntu1 [15.8 MB] Get:94 http://ftpmaster.internal/ubuntu jammy/main armhf libstdc++-11-dev armhf 11.2.0-13ubuntu1 [2181 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/main armhf libgcc-11-dev armhf 11.2.0-13ubuntu1 [838 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main armhf libisl23 armhf 0.24-2 [581 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main armhf libmpc3 armhf 1.2.1-1 [39.5 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main armhf libctf0 armhf 2.37-10ubuntu1 [93.7 kB] Get:99 http://ftpmaster.internal/ubuntu jammy/main armhf libctf-nobfd0 armhf 2.37-10ubuntu1 [93.8 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main armhf binutils-arm-linux-gnueabihf armhf 2.37-10ubuntu1 [3057 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/main armhf libbinutils armhf 2.37-10ubuntu1 [492 kB] Get:102 http://ftpmaster.internal/ubuntu jammy/main armhf binutils armhf 2.37-10ubuntu1 [3174 B] Get:103 http://ftpmaster.internal/ubuntu jammy/main armhf binutils-common armhf 2.37-10ubuntu1 [213 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main armhf cpp-11 armhf 11.2.0-13ubuntu1 [7837 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11-base armhf 11.2.0-13ubuntu1 [21.1 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main armhf libss2 armhf 1.46.5-2ubuntu1 [10.1 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/main armhf sensible-utils all 0.0.17 [20.1 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main armhf usrmerge all 25ubuntu2 [54.7 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/main armhf openssl armhf 3.0.1-0ubuntu1 [1150 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/main armhf ca-certificates all 20211016 [148 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/main armhf libgdbm6 armhf 1.22-1 [31.0 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main armhf make armhf 4.3-4ubuntu2 [162 kB] Get:113 http://ftpmaster.internal/ubuntu jammy/main armhf lto-disabled-list all 18 [12.2 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/main armhf python3-psutil armhf 5.8.0-2 [156 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/main armhf gpg armhf 2.2.27-3ubuntu1 [483 kB] Get:116 http://ftpmaster.internal/ubuntu jammy/main armhf gpgconf armhf 2.2.27-3ubuntu1 [115 kB] Get:117 http://ftpmaster.internal/ubuntu jammy/main armhf gpg-agent armhf 2.2.27-3ubuntu1 [227 kB] Get:118 http://ftpmaster.internal/ubuntu jammy/main armhf libgdbm-compat4 armhf 1.22-1 [6076 B] Get:119 http://ftpmaster.internal/ubuntu jammy/main armhf lockfile-progs armhf 0.1.19 [9508 B] Get:120 http://ftpmaster.internal/ubuntu jammy/main armhf pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 73.7 MB in 2s (40.8 MB/s) (Reading database ... 12985 files and directories currently installed.) 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Setting up libsqlite3-0:armhf (3.36.0-2) ... Setting up binutils-common:armhf (2.37-10ubuntu1) ... Setting up libctf-nobfd0:armhf (2.37-10ubuntu1) ... Setting up libgomp1:armhf (12-20220106-1ubuntu1) ... Setting up bzip2 (1.0.8-5) ... Setting up libasan6:armhf (11.2.0-13ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jan 15 00:12:07 UTC 2022. Universal Time is now: Sat Jan 15 00:12:07 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:armhf (6.3-1) ... Setting up libmpc3:armhf (1.2.1-1) ... Setting up systemd-timesyncd (249.5-2ubuntu3) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:armhf (12-20220106-1ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:armhf (1.46.5-2ubuntu1) ... Setting up libncursesw6:armhf (6.3-1) ... Setting up libdpkg-perl (1.21.1ubuntu11) ... Setting up logsave (1.46.5-2ubuntu1) ... 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Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up libgdbm-compat4:armhf (1.22-1) ... Setting up libstdc++-11-dev:armhf (11.2.0-13ubuntu1) ... Setting up gpgconf (2.2.27-3ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.37-10ubuntu1) ... Setting up gpg (2.2.27-3ubuntu1) ... Setting up libpython3.9-stdlib:armhf (3.9.9-2) ... Setting up libpython3-stdlib:armhf (3.9.7-4) ... Setting up gpg-agent (2.2.27-3ubuntu1) ... Setting up binutils (2.37-10ubuntu1) ... Setting up gcc-11 (11.2.0-13ubuntu1) ... Setting up python3.9 (3.9.9-2) ... Setting up g++-11 (11.2.0-13ubuntu1) ... Setting up python3 (3.9.7-4) ... Setting up python3-psutil (5.8.0-2) ... Setting up dpkg-dev (1.21.1ubuntu11) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22765110 armhf jammy -c chroot:build-PACKAGEBUILD-22765110 --arch=armhf --dist=jammy --nolog gemmi_0.5.1+ds-1.dsc Initiating build PACKAGEBUILD-22765110 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-166-generic #174-Ubuntu SMP Wed Dec 8 19:08:37 UTC 2021 armv7l sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-071.buildd +==============================================================================+ | gemmi 0.5.1+ds-1 (armhf) Sat, 15 Jan 2022 00:12:18 +0000 | +==============================================================================+ Package: gemmi Version: 0.5.1+ds-1 Source Version: 0.5.1+ds-1 Distribution: jammy Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22765110/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gemmi_0.5.1+ds-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/gemmi-IOtRQG/gemmi-0.5.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/gemmi-IOtRQG' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Lzyxbl/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-Lzyxbl/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Lzyxbl/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-Lzyxbl/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Lzyxbl/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-Lzyxbl/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (59.9 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded. Need to get 650 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Lzyxbl/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [650 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 650 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13937 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), dh-python, help2man, libstb-dev, python3-dev, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev Filtered Build-Depends: cmake, debhelper-compat (= 13), dh-python, help2man, libstb-dev, python3-dev, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-gemmi-dummy' in '/<>/resolver-Lzyxbl/apt_archive/sbuild-build-depends-gemmi-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gemmi-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-Lzyxbl/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Lzyxbl/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Lzyxbl/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Lzyxbl/apt_archive ./ Sources [567 B] Get:5 copy:/<>/resolver-Lzyxbl/apt_archive ./ Packages [640 B] Fetched 2170 B in 0s (67.0 kB/s) Reading package lists... Reading package lists... Install gemmi build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-elpa-helper dh-python dh-strip-nondeterminism dwz emacsen-common file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libcurl4 libdebhelper-perl libdw1 libelf1 libexpat1-dev libfile-stripnondeterminism-perl libicu67 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp25 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython3-dev libpython3.9 libpython3.9-dev librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libstb-dev libstb0 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf pybind11-dev python3-attr python3-dev python3-distutils python3-importlib-metadata python3-iniconfig python3-lib2to3 python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pybind11 python3-pyparsing python3-pytest python3-toml python3-zipp python3.9-dev tao-pegtl-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build cmake-format dh-make flit python3-build python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl pybind11-doc python-attr-doc python3-setuptools subversion python-pyparsing-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl libeigen3-dev python3-numpy python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-elpa-helper dh-python dh-strip-nondeterminism dwz emacsen-common file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libcurl4 libdebhelper-perl libdw1 libelf1 libexpat1-dev libfile-stripnondeterminism-perl libicu67 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp25 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython3-dev libpython3.9 libpython3.9-dev librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libstb-dev libstb0 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf pybind11-dev python3-attr python3-dev python3-distutils python3-importlib-metadata python3-iniconfig python3-lib2to3 python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pybind11 python3-pyparsing python3-pytest python3-toml python3-zipp python3.9-dev sbuild-build-depends-gemmi-dummy tao-pegtl-dev zlib1g-dev 0 upgraded, 82 newly installed, 0 to remove and 3 not upgraded. Need to get 34.4 MB of archives. After this operation, 118 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Lzyxbl/apt_archive ./ sbuild-build-depends-gemmi-dummy 0.invalid.0 [728 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf liblocale-gettext-perl armhf 1.07-4build2 [16.3 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main armhf libelf1 armhf 0.186-1 [43.2 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main armhf libicu67 armhf 67.1-7ubuntu1 [9788 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf libxml2 armhf 2.9.12+dfsg-5 [598 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf python3-pkg-resources all 58.2.0-1 [130 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf bsdextrautils armhf 2.37.2-4ubuntu1 [77.1 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf libmagic-mgc armhf 1:5.41-2 [257 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf libmagic1 armhf 1:5.41-2 [80.2 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main armhf file armhf 1:5.41-2 [20.6 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main armhf gettext-base armhf 0.21-4ubuntu3 [36.0 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main armhf libuchardet0 armhf 0.0.7-1build1 [75.6 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf groff-base armhf 1.22.4-8 [870 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main armhf libpipeline1 armhf 1.5.5-1 [25.6 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf libpsl5 armhf 0.21.0-1.2build1 [56.1 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main armhf libuv1 armhf 1.42.0-1 [76.6 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main armhf man-db armhf 2.9.4-4 [1142 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf libsigsegv2 armhf 2.13-1ubuntu2 [13.7 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf m4 armhf 1.4.18-5ubuntu1 [192 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf autoconf all 2.71-2 [338 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main armhf autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main armhf automake all 1:1.16.5-1.1 [558 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main armhf autopoint all 0.21-4ubuntu3 [422 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf libarchive13 armhf 3.5.2-1 [329 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf libbrotli1 armhf 1.0.9-2build4 [306 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf libsasl2-modules-db armhf 2.1.27+dfsg2-3 [19.1 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf libsasl2-2 armhf 2.1.27+dfsg2-3 [50.8 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf libldap-2.5-0 armhf 2.5.6+dfsg-1~exp1ubuntu1 [162 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf libnghttp2-14 armhf 1.43.0-1build2 [70.1 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build3 [53.0 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf libssh-4 armhf 0.9.6-2 [163 kB] 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libarchive-zip-perl all 1.68-1 [90.2 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:44 http://ftpmaster.internal/ubuntu jammy/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main armhf dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:46 http://ftpmaster.internal/ubuntu jammy/main armhf libdw1 armhf 0.186-1 [228 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main armhf debugedit armhf 1:5.0-4 [43.2 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main armhf dwz armhf 0.14-1build1 [99.2 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main armhf gettext armhf 0.21-4ubuntu3 [755 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main armhf debhelper all 13.5.2ubuntu1 [926 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main armhf python3-lib2to3 all 3.9.9-3 [77.7 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main armhf python3-distutils all 3.9.9-3 [144 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/universe armhf dh-python all 5.20220101 [103 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/universe armhf help2man armhf 1.48.5 [139 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main armhf libexpat1-dev armhf 2.4.2-1 [126 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-8 [321 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main armhf libjs-underscore all 1.9.1~dfsg-4 [103 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main armhf libjs-sphinxdoc all 4.3.2-1 [139 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.9 armhf 3.9.9-2 [1678 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu7 [157 kB] Get:63 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http://ftpmaster.internal/ubuntu jammy/main armhf python3-importlib-metadata all 4.6.4-1 [16.2 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-iniconfig all 1.1.1-1 [5960 B] Get:75 http://ftpmaster.internal/ubuntu jammy/main armhf python3-pyparsing all 2.4.7-1 [61.4 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main armhf python3-packaging all 21.3-1 [30.7 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pluggy all 0.13.0-7.1 [19.0 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-py all 1.10.0-1 [71.9 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pybind11 all 2.7.1-2 [148 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-toml all 0.10.2-1 [16.5 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/universe armhf python3-pytest all 6.2.5-1ubuntu1 [214 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/universe armhf tao-pegtl-dev all 2.8.3-3 [49.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.4 MB in 3s (12.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-166-generic arm64 (armv7l) Toolchain package versions: binutils_2.37-10ubuntu1 dpkg-dev_1.21.1ubuntu11 g++-11_11.2.0-13ubuntu1 gcc-11_11.2.0-13ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-13ubuntu1 libstdc++6_12-20220106-1ubuntu1 linux-libc-dev_5.13.0-19.19 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.14 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-6ubuntu1 binutils_2.37-10ubuntu1 binutils-arm-linux-gnueabihf_2.37-10ubuntu1 binutils-common_2.37-10ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 cmake_3.22.1-1ubuntu1 cmake-data_3.22.1-1ubuntu1 coreutils_8.32-4ubuntu3 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-13ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2ubuntu1 debianutils_5.5-1ubuntu1 debugedit_1:5.0-4 dh-autoreconf_20 dh-elpa-helper_2.0.9ubuntu1 dh-python_5.20220101 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu1 dpkg_1.21.1ubuntu11 dpkg-dev_1.21.1ubuntu11 dwz_0.14-1build1 e2fsprogs_1.46.5-2ubuntu1 emacsen-common_3.0.4 fakeroot_1.25.3-1.1ubuntu3 file_1:5.41-2 findutils_4.8.0-1ubuntu2 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-13ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-13ubuntu1 gcc-11-base_11.2.0-13ubuntu1 gcc-12-base_12-20220106-1ubuntu1 gettext_0.21-4ubuntu3 gettext-base_0.21-4ubuntu3 gpg_2.2.27-3ubuntu1 gpg-agent_2.2.27-3ubuntu1 gpgconf_2.2.27-3ubuntu1 gpgv_2.2.27-3ubuntu1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4ubuntu2 help2man_1.48.5 hostname_3.23ubuntu1 init_1.61 init-system-helpers_1.61 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10ubuntu2 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libfakeroot_1.25.3-1.1ubuntu3 libffi8_3.4.2-1ubuntu5 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.2.0-13ubuntu1 libgcc-s1_12-20220106-1ubuntu1 libgcrypt20_1.9.4-3ubuntu2 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-1ubuntu3 libgnutls30_3.7.2-5ubuntu1 libgomp1_12-20220106-1ubuntu1 libgpg-error0_1.43-1 libgssapi-krb5-2_1.19.2-0ubuntu1 libhogweed6_3.7.3-1build1 libicu67_67.1-7ubuntu1 libidn2-0_2.3.2-2 libip4tc2_1.8.7-1ubuntu4 libisl23_0.24-2 libjs-jquery_3.5.1+dfsg+~3.5.5-8 libjs-sphinxdoc_4.3.2-1 libjs-underscore_1.9.1~dfsg-4 libjson-c5_0.15-2build3 libjsoncpp25_1.9.5-2 libk5crypto3_1.19.2-0ubuntu1 libkeyutils1_1.6.1-2ubuntu2 libkmod2_28-1ubuntu5 libkrb5-3_1.19.2-0ubuntu1 libkrb5support0_1.19.2-0ubuntu1 libldap-2.5-0_2.5.6+dfsg-1~exp1ubuntu1 liblocale-gettext-perl_1.07-4build2 liblockfile-bin_1.17-1build1 liblockfile1_1.17-1build1 liblz4-1_1.9.3-2build1 liblzma5_5.2.5-2build1 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmount1_2.37.2-4ubuntu1 libmpc3_1.2.1-1 libmpdec3_2.5.1-2build1 libmpfr6_4.1.0-3build2 libncurses6_6.3-1 libncursesw6_6.3-1 libnettle8_3.7.3-1build1 libnghttp2-14_1.43.0-1build2 libnpth0_1.6-3build1 libnsl-dev_1.3.0-2build1 libnsl2_1.3.0-2build1 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-10ubuntu2 libpam-modules-bin_1.4.0-10ubuntu2 libpam-runtime_1.4.0-10ubuntu2 libpam0g_1.4.0-10ubuntu2 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13build4 libperl5.32_5.32.1-3ubuntu3 libpipeline1_1.5.5-1 libpng16-16_1.6.37-3build4 libprocps8_2:3.3.17-5ubuntu3 libpsl5_0.21.0-1.2build1 libpython3-dev_3.9.7-4 libpython3-stdlib_3.9.7-4 libpython3.9_3.9.9-2 libpython3.9-dev_3.9.9-2 libpython3.9-minimal_3.9.9-2 libpython3.9-stdlib_3.9.9-2 libreadline8_8.1.2-1 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2build3 libsasl2-2_2.1.27+dfsg2-3 libsasl2-modules-db_2.1.27+dfsg2-3 libseccomp2_2.5.2-2ubuntu2 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1ubuntu2 libsepol2_3.3-1 libsigsegv2_2.13-1ubuntu2 libsmartcols1_2.37.2-4ubuntu1 libsqlite3-0_3.36.0-2 libss2_1.46.5-2ubuntu1 libssh-4_0.9.6-2 libssl1.1_1.1.1l-1ubuntu1 libssl3_3.0.1-0ubuntu1 libstb-dev_0.0~git20200713.b42009b+ds-1 libstb0_0.0~git20200713.b42009b+ds-1 libstdc++-11-dev_11.2.0-13ubuntu1 libstdc++6_12-20220106-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_249.5-2ubuntu3 libtasn1-6_4.18.0-4 libtinfo6_6.3-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15build1 libubsan1_12-20220106-1ubuntu1 libuchardet0_0.0.7-1build1 libudev1_249.5-2ubuntu3 libunistring2_0.9.10-6 libuuid1_2.37.2-4ubuntu1 libuv1_1.42.0-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2build1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.13.0-19.19 lockfile-progs_0.1.19 login_1:4.8.1-2ubuntu1 logsave_1.46.5-2ubuntu1 lsb-base_11.1.0ubuntu3 lto-disabled-list_18 m4_1.4.18-5ubuntu1 make_4.3-4ubuntu2 man-db_2.9.4-4 mawk_1.3.4.20200120-2build1 media-types_4.0.0 mount_2.37.2-4ubuntu1 ncurses-base_6.3-1 ncurses-bin_6.3-1 openssl_3.0.1-0ubuntu1 optipng_0.7.7-2 passwd_1:4.8.1-2ubuntu1 patch_2.7.6-7build1 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1build1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 pybind11-dev_2.7.1-2 python3_3.9.7-4 python3-attr_20.3.0-1ubuntu1 python3-dev_3.9.7-4 python3-distutils_3.9.9-3 python3-importlib-metadata_4.6.4-1 python3-iniconfig_1.1.1-1 python3-lib2to3_3.9.9-3 python3-minimal_3.9.7-4 python3-more-itertools_8.10.0-2 python3-packaging_21.3-1 python3-pkg-resources_58.2.0-1 python3-pluggy_0.13.0-7.1 python3-psutil_5.8.0-2 python3-py_1.10.0-1 python3-pybind11_2.7.1-2 python3-pyparsing_2.4.7-1 python3-pytest_6.2.5-1ubuntu1 python3-toml_0.10.2-1 python3-zipp_1.0.0-3 python3.9_3.9.9-2 python3.9-dev_3.9.9-2 python3.9-minimal_3.9.9-2 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-0ubuntu5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gemmi-dummy_0.invalid.0 sed_4.8-1ubuntu1 sensible-utils_0.0.17 systemd_249.5-2ubuntu3 systemd-sysv_249.5-2ubuntu3 systemd-timesyncd_249.5-2ubuntu3 sysvinit-utils_2.96-7ubuntu2 tao-pegtl-dev_2.8.3-3 tar_1.34+dfsg-1build2 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Dec 14 08:00:01 2021 UTC gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./gemmi_0.5.1+ds-1.dsc dpkg-source: info: extracting gemmi in /<>/gemmi-0.5.1+ds dpkg-source: info: unpacking gemmi_0.5.1+ds.orig.tar.xz dpkg-source: info: unpacking gemmi_0.5.1+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-tao-pegtl.patch dpkg-source: info: applying change_error_type_in_test.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-22765110 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22765110 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22765110 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage.pl: info: source package gemmi dpkg-buildpackage.pl: info: source version 0.5.1+ds-1 dpkg-buildpackage.pl: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage.pl: info: host architecture armhf debian/rules clean dh clean --buildsystem=cmake --with python3 dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary-arch dh binary-arch --buildsystem=cmake --with python3 dh_update_autotools_config -a -O--buildsystem=cmake dh_autoreconf -a -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/gemmi-0.5.1+ds' dh_auto_configure -- -DUSE_PYTHON=1 -DINSTALL_EGG_INFO=OFF cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DUSE_PYTHON=1 -DINSTALL_EGG_INFO=OFF .. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Skipping Fortran bindings. Add -D USE_FORTRAN=1 to build them. -- Compiling with C++ standard: 17 -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11") -- Benchmarks not configured. -- The python module will be built. -- Found PythonInterp: /usr/bin/python3.9 (found version "3.9.9") -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.7.1" ) -- Found pybind11 2.7.1: /usr/include;/usr/include/python3.9 -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf make[1]: Leaving directory '/<>/gemmi-0.5.1+ds' dh_auto_build -a -O--buildsystem=cmake cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<>/gemmi-0.5.1+ds -B/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/gemmi-0.5.1+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 -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/depend make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/depend make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/input.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/options.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/mapcoef.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/output.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/build make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 0%] Building CXX object CMakeFiles/input.dir/src/input.cpp.o [ 2%] Building CXX object CMakeFiles/options.dir/src/options.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/input.cpp [ 4%] Building CXX object CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/options.cpp /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/mapcoef.cpp [ 7%] Building CXX object CMakeFiles/output.dir/src/output.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/output.cpp In file included from /<>/gemmi-0.5.1+ds/src/output.cpp:6: /<>/gemmi-0.5.1+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 '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 7%] Built target options make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/depend make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/py.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/build make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 7%] Building CXX object CMakeFiles/py.dir/python/mol.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/mol.cpp In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/fileutil.hpp:16, from /<>/gemmi-0.5.1+ds/include/gemmi/gz.hpp:14, from /<>/gemmi-0.5.1+ds/src/mapcoef.cpp:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/read_cif.hpp:14, from /<>/gemmi-0.5.1+ds/src/input.cpp:4: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 7%] Built target mapcoef [ 9%] Building CXX object CMakeFiles/py.dir/python/gemmi.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/gemmi.cpp In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/read_cif.hpp:14, from /<>/gemmi-0.5.1+ds/src/input.cpp:4: /usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/read_cif.hpp:14, from /<>/gemmi-0.5.1+ds/src/input.cpp:4: /usr/include/c++/11/bits/vector.tcc: In function ‘gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 9%] Built target output [ 12%] Building CXX object CMakeFiles/py.dir/python/align.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/align.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /<>/gemmi-0.5.1+ds/python/align.cpp:5: /<>/gemmi-0.5.1+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." | ^~~~~~~ [ 14%] Building CXX object CMakeFiles/py.dir/python/ccp4.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/ccp4.cpp [ 14%] Building CXX object CMakeFiles/py.dir/python/chemcomp.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/chemcomp.cpp make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 14%] Built target input make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/depend make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/program.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/build make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 17%] Building CXX object CMakeFiles/program.dir/src/align.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/align.cpp [ 19%] Building CXX object CMakeFiles/py.dir/python/cif.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/cif.cpp [ 21%] Building CXX object CMakeFiles/py.dir/python/custom.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/custom.cpp In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/model.hpp:8, from /<>/gemmi-0.5.1+ds/src/align.cpp:5: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Position&}; _Tp = gemmi::Position; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/model.hpp:8, from /<>/gemmi-0.5.1+ds/src/align.cpp:5: /usr/include/c++/11/bits/stl_vector.h: In function ‘gemmi::SupResult gemmi::calculate_superposition(gemmi::ConstResidueSpan, gemmi::ConstResidueSpan, gemmi::PolymerType, gemmi::SupSelect, int, double, char, bool)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 21%] Building CXX object CMakeFiles/py.dir/python/elem.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/elem.cpp [ 24%] Building CXX object CMakeFiles/program.dir/src/blobs.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/blobs.cpp In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/src/blobs.cpp:4: /usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Blob; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<{anonymous}::run(OptParser&):: >]’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/src/blobs.cpp:4: /usr/include/c++/11/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<{anonymous}::run(OptParser&):: >]’: /usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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<{anonymous}::run(OptParser&):: >]’: /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/blobs.cpp:4: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Blob&}; _Tp = gemmi::Blob; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 26%] Building CXX object CMakeFiles/py.dir/python/grid.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/grid.cpp /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Transform&}; _Tp = gemmi::Transform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Fractional&}; _Tp = gemmi::Fractional; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/blobs.cpp:4: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::NeighborSearch::add_site(const gemmi::SmallStructure::Site&, int)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/blobs.cpp:4: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/blobs.cpp:4: /usr/include/c++/11/bits/stl_vector.h: In function ‘std::vector gemmi::find_blobs_by_flood_fill(const gemmi::Grid&, const gemmi::BlobCriteria&)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In function ‘void gemmi::expand_ncs(gemmi::Structure&, gemmi::HowToNameCopiedChain)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::NeighborSearch::initialize(gemmi::Model&, const gemmi::UnitCell&, double)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/blobs.cpp:4: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/src/blobs.cpp:4: /usr/include/c++/11/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<{anonymous}::run(OptParser&):: >]’: /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In function ‘int {anonymous}::run(OptParser&)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object CMakeFiles/py.dir/python/hkl.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/hkl.cpp [ 29%] Building CXX object CMakeFiles/program.dir/src/cif2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/cif2mtz.cpp [ 31%] Building CXX object CMakeFiles/py.dir/python/meta.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/meta.cpp In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/read_cif.hpp:14, from /<>/gemmi-0.5.1+ds/src/cif2mtz.cpp:12: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘gemmi::Mtz::Dataset& gemmi::Mtz::add_dataset(const string&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector gemmi::as_refln_blocks(std::vector&&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object CMakeFiles/program.dir/src/cif2json.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/cif2json.cpp [ 34%] Building CXX object CMakeFiles/py.dir/python/monlib.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/monlib.cpp [ 36%] Building CXX object CMakeFiles/program.dir/src/contact.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/contact.cpp [ 39%] Building CXX object CMakeFiles/py.dir/python/mtz.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/mtz.cpp In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/contact.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Transform&}; _Tp = gemmi::Transform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Fractional&}; _Tp = gemmi::Fractional; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/contact.cpp:7: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::NeighborSearch::add_site(const gemmi::SmallStructure::Site&, int)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/contact.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/contact.cpp:7: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::NeighborSearch::initialize(gemmi::Model&, const gemmi::UnitCell&, double)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/contact.cpp:7: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object CMakeFiles/program.dir/src/contents.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/contents.cpp [ 43%] Building CXX object CMakeFiles/py.dir/python/read.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/read.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/smcif.hpp:12, from /<>/gemmi-0.5.1+ds/python/read.cpp:7: /<>/gemmi-0.5.1+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/recgrid.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/recgrid.cpp In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/symmetry.hpp:15, from /<>/gemmi-0.5.1+ds/src/contents.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘int contents_main(int, char**)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object CMakeFiles/program.dir/src/convert.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/convert.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /<>/gemmi-0.5.1+ds/src/convert.cpp:16: /<>/gemmi-0.5.1+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." | ^~~~~~~ [ 46%] Building CXX object CMakeFiles/py.dir/python/scaling.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/scaling.cpp [ 48%] Building CXX object CMakeFiles/py.dir/python/search.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/search.cpp In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::BasicRefinementInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ReflectionsInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 [ 51%] Building CXX object CMakeFiles/py.dir/python/sf.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/sf.cpp /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Transform&}; _Tp = gemmi::Transform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Fractional&}; _Tp = gemmi::Fractional; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::NeighborSearch::add_site(const gemmi::SmallStructure::Site&, int)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::Selection::remove_selected(T&) const [with T = gemmi::Model]’: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In function ‘void gemmi::remove_hydrogens(T&) [with T = gemmi::Structure]’: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::impl::parse_cid(const string&, gemmi::Selection&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::pdb_impl::read_remark_200_230_240(const char*, gemmi::Metadata&, std::string*&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/stl_vector.h: In function ‘void gemmi::expand_ncs(gemmi::Structure&, gemmi::HowToNameCopiedChain)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 51%] Building CXX object CMakeFiles/py.dir/python/sym.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/sym.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/it92.hpp:16, from /<>/gemmi-0.5.1+ds/python/sf.cpp:6: /<>/gemmi-0.5.1+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]’: /<>/gemmi-0.5.1+ds/include/gemmi/dencalc.hpp:19:54: required from ‘double gemmi::determine_cutoff_radius(double, const PrecalExpSum&, double) [with PrecalExpSum = gemmi::ExpSum<5, double>]’ /<>/gemmi-0.5.1+ds/include/gemmi/dencalc.hpp:121:35: 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>]’ /<>/gemmi-0.5.1+ds/python/sf.cpp:62:36: required from ‘void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]’ /<>/gemmi-0.5.1+ds/python/sf.cpp:83:20: required from here /<>/gemmi-0.5.1+ds/include/gemmi/formfact.hpp:27:24: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 27 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::NeighborSearch::initialize(gemmi::Model&, const gemmi::UnitCell&, double)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::Selection::remove_not_selected(T&) const [with T = gemmi::Structure]’: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const char*&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::pdb_impl::add_restraint_count_weight(gemmi::RefinementInfo&, const char*, const char*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘T& gemmi::impl::find_or_add(std::vector&, const string&) [with T = gemmi::RefinementInfo::Restr]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::pdb_impl::read_remark3_line(const char*, gemmi::Metadata&, std::string*&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/to_cif.hpp:9, from /<>/gemmi-0.5.1+ds/src/convert.cpp:3: /usr/include/c++/11/bits/stl_vector.h: In function ‘int convert_main(int, char**)’: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | 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/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/topo.cpp [ 56%] Building CXX object CMakeFiles/program.dir/src/fprime.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/fprime.cpp In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/fprime.hpp:24, from /<>/gemmi-0.5.1+ds/src/fprime.cpp:4: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘int fprime_main(int, char**)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building CXX object CMakeFiles/program.dir/src/grep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/grep.cpp [ 60%] Building CXX object CMakeFiles/py.dir/python/unitcell.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/unitcell.cpp [ 60%] Building CXX object CMakeFiles/py.dir/python/write.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.9 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/python/write.cpp In file included from /<>/gemmi-0.5.1+ds/python/write.cpp:4: /<>/gemmi-0.5.1+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." | ^~~~~~~ [ 60%] Building CXX object CMakeFiles/program.dir/src/h.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/h.cpp [ 63%] Building CXX object CMakeFiles/program.dir/src/json2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/json2cif.cpp [ 65%] Building CXX object CMakeFiles/program.dir/src/main.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/main.cpp [ 68%] Building CXX object CMakeFiles/program.dir/src/map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/map.cpp [ 68%] Building CXX object CMakeFiles/program.dir/src/map2sf.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/map2sf.cpp [ 70%] Linking CXX shared module gemmi.cpython-39-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=/<>/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -flto -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o gemmi.cpython-39-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 In file included from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/c++/11/stdexcept:39, from /<>/gemmi-0.5.1+ds/src/h.cpp:5: /usr/include/c++/11/bits/stl_algobase.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]’: /usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2061 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:11, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 [ 73%] Building CXX object CMakeFiles/program.dir/src/mask.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/mask.cpp In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:11, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/grid.hpp:11, from /<>/gemmi-0.5.1+ds/src/map2sf.cpp:12: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/stl_vector.h: In function ‘void gemmi::add_hydrogens_without_positions(const gemmi::ChemComp&, gemmi::Residue&)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 [ 75%] Building CXX object CMakeFiles/program.dir/src/merge.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/merge.cpp /usr/include/c++/11/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:11, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/stl_algo.h: In function ‘_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(gemmi::Residue&):: >]’: /usr/include/c++/11/bits/stl_algo.h:813:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 813 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:813:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h: In function ‘void gemmi::remove_hydrogens(T&) [with T = gemmi::Structure]’: /usr/include/c++/11/bits/stl_algo.h:894:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 894 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 895 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:24, from /<>/gemmi-0.5.1+ds/src/merge.cpp:14: /<>/gemmi-0.5.1+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++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/c++/11/stdexcept:39, from /<>/gemmi-0.5.1+ds/src/h.cpp:5: /usr/include/c++/11/bits/stl_algobase.h: In member function ‘gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const string&)’: /usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2114 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2115 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Angle&}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Mtz::read_main_headers(Stream&) [with Stream = gemmi::FileStream]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::place_hydrogens(const gemmi::Topo&, const gemmi::Atom&)::BondedAtom}; _Tp = gemmi::place_hydrogens(const gemmi::Topo&, const gemmi::Atom&)::BondedAtom; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::place_hydrogens(const gemmi::Topo&, const gemmi::Atom&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::impl::read_connectivity(gemmi::cif::Block&, gemmi::Structure&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Bond&}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Torsion&}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 [ 75%] Building CXX object CMakeFiles/program.dir/src/mondiff.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/mondiff.cpp In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from /usr/include/c++/11/stdexcept:39, from /<>/gemmi-0.5.1+ds/src/h.cpp:5: /usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2114 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2115 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/bits/stl_vector.h: In function ‘void gemmi::vector_remove_if(std::vector&, F&&) [with T = gemmi::Intensities::Refl; F = gemmi::Intensities::remove_systematic_absences()::]’: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/vector.tcc: In function ‘gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::MtzDataProxy]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_unmerged_intensities_from_xds(const gemmi::XdsAscii&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_mean_intensities_from_mtz(const gemmi::Mtz&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_unmerged_intensities_from_mtz(const gemmi::Mtz&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:66, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; bool _TrivialValueTypes = false]’: /usr/include/c++/11/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 85 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_uninitialized.h: In copy constructor ‘gemmi::Restraints::Restraints(const gemmi::Restraints&)’: /usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 148 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 151 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector gemmi::as_refln_blocks(std::vector&&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_uninitialized.h: In member function ‘void gemmi::Topo::initialize_refmac_topology(const gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)’: /usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 148 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 151 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_tree.h:63, from /usr/include/c++/11/set:60, from /<>/gemmi-0.5.1+ds/src/mondiff.cpp:7: /usr/include/c++/11/bits/stl_algobase.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const gemmi::Restraints::AtomId&, const gemmi::Restraints::AtomId&):: >]’: /usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2061 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::XdsAscii::read_stream(Stream&&, const string&) [with Stream = gemmi::FileStream]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:21, from /<>/gemmi-0.5.1+ds/src/merge.cpp:14: /<>/gemmi-0.5.1+ds/include/gemmi/xds_ascii.hpp:212:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 212 | } | ^ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::XdsAscii::read_stream(Stream&&, const string&) [with Stream = gemmi::MaybeGzipped::GzStream]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:21, from /<>/gemmi-0.5.1+ds/src/merge.cpp:14: /<>/gemmi-0.5.1+ds/include/gemmi/xds_ascii.hpp:212:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 212 | } | ^ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_data(const DataProxy&, size_t, size_t) [with DataProxy = gemmi::ReflnDataProxy]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::ReflnDataProxy]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algobase.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const gemmi::Restraints::AtomId&, const gemmi::Restraints::AtomId&, const gemmi::Restraints::AtomId&, const gemmi::Restraints::AtomId&):: >]’: /usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:11, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In function ‘std::unique_ptr gemmi::prepare_topology(gemmi::Structure&, gemmi::MonLib&, size_t, gemmi::HydrogenChange, bool, std::ostream*, bool)’: /usr/include/c++/11/bits/stl_algo.h:894:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 894 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 895 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:11, from /<>/gemmi-0.5.1+ds/include/gemmi/mmcif.hpp:11, from /<>/gemmi-0.5.1+ds/src/h.cpp:7: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/chemcomp.hpp:10, from /<>/gemmi-0.5.1+ds/src/mondiff.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘gemmi::ChemComp gemmi::make_chemcomp_from_block(const gemmi::cif::Block&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In member function ‘void gemmi::Intensities::merge_in_place(gemmi::Intensities::Type)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_tree.h:63, from /usr/include/c++/11/set:60, from /<>/gemmi-0.5.1+ds/src/mondiff.cpp:7: /usr/include/c++/11/bits/stl_algobase.h: In function ‘int mondiff_main(int, char**)’: /usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2114 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2115 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2114 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2115 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2114 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2115 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2114 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2115 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/src/merge.cpp:8: /usr/include/c++/11/bits/stl_algo.h: In function ‘int merge_main(int, char**)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 78%] Building CXX object CMakeFiles/program.dir/src/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/mtz.cpp [ 80%] Building CXX object CMakeFiles/program.dir/src/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:24, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /<>/gemmi-0.5.1+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/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/reindex.cpp In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/src/reindex.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘gemmi::UnitCell gemmi::UnitCell::changed_basis_backward(const gemmi::Op&, bool)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/bits/stl_vector.h: In function ‘void gemmi::vector_remove_if(std::vector&, F&&) [with T = gemmi::Intensities::Refl; F = gemmi::Intensities::remove_systematic_absences()::]’: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::MtzDataProxy]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_unmerged_intensities_from_xds(const gemmi::XdsAscii&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_mean_intensities_from_mtz(const gemmi::Mtz&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_unmerged_intensities_from_mtz(const gemmi::Mtz&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_mean_intensities_from_mmcif(const gemmi::ReflnBlock&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Intensities::read_anomalous_data(const DataProxy&, int, size_t (&)[2], size_t (&)[2]) [with DataProxy = gemmi::ReflnDataProxy]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object CMakeFiles/program.dir/src/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/residues.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /<>/gemmi-0.5.1+ds/src/residues.cpp:5: /<>/gemmi-0.5.1+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++/11/bits/vector.tcc: In member function ‘void gemmi::XdsAscii::read_stream(Stream&&, const string&) [with Stream = gemmi::FileStream]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object CMakeFiles/program.dir/src/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/rmsz.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:21, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /<>/gemmi-0.5.1+ds/include/gemmi/xds_ascii.hpp:212:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 212 | } | ^ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::XdsAscii::read_stream(Stream&&, const string&) [with Stream = gemmi::MaybeGzipped::GzStream]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:21, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /<>/gemmi-0.5.1+ds/include/gemmi/xds_ascii.hpp:212:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 212 | } | ^ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In member function ‘void gemmi::Intensities::merge_in_place(gemmi::Intensities::Type)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:17, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /usr/include/c++/11/bits/stl_algo.h: In function ‘bool gemmi::validate_merged_intensities(gemmi::Intensities&, gemmi::Intensities&, bool, std::ostream&)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/select.hpp:13, from /<>/gemmi-0.5.1+ds/src/residues.cpp:5: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object CMakeFiles/program.dir/src/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/sf2map.cpp /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::impl::parse_cid(const string&, gemmi::Selection&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /<>/gemmi-0.5.1+ds/src/sf2map.cpp:8: /<>/gemmi-0.5.1+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++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /<>/gemmi-0.5.1+ds/src/rmsz.cpp:5: /usr/include/c++/11/bits/stl_algobase.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]’: /usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2061 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/11/bits/stl_algobase.h:2061:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 [ 87%] Building CXX object CMakeFiles/program.dir/src/sfcalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/sfcalc.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/smcif.hpp:12, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:19: /<>/gemmi-0.5.1+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++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/model.hpp:8, from /<>/gemmi-0.5.1+ds/src/rmsz.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /<>/gemmi-0.5.1+ds/src/rmsz.cpp:5: /usr/include/c++/11/bits/stl_algobase.h: In member function ‘gemmi::Restraints::Plane& gemmi::Restraints::get_or_add_plane(const string&)’: /usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2114 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2115 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/model.hpp:8, from /<>/gemmi-0.5.1+ds/src/rmsz.cpp:7: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Angle&}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/ccp4.hpp:16, from /<>/gemmi-0.5.1+ds/src/sf2map.cpp:6: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /<>/gemmi-0.5.1+ds/include/gemmi/it92.hpp:16, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:12: /<>/gemmi-0.5.1+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]’: /<>/gemmi-0.5.1+ds/include/gemmi/dencalc.hpp:19:54: required from ‘double gemmi::determine_cutoff_radius(double, const PrecalExpSum&, double) [with PrecalExpSum = gemmi::ExpSum<5, double>]’ /<>/gemmi-0.5.1+ds/include/gemmi/dencalc.hpp:121:35: 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>]’ /<>/gemmi-0.5.1+ds/include/gemmi/dencalc.hpp:131:38: required from ‘void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<4, 1, double>; Table = gemmi::IT92; Real = float]’ /<>/gemmi-0.5.1+ds/include/gemmi/dencalc.hpp:107:32: required from ‘void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::IT92; Real = float]’ /<>/gemmi-0.5.1+ds/include/gemmi/dencalc.hpp:163:11: required from ‘void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::IT92; Real = float]’ /<>/gemmi-0.5.1+ds/include/gemmi/dencalc.hpp:168:5: required from ‘void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::IT92; Real = float]’ /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:207:36: required from ‘void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const {anonymous}::RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::IT92; Real = float]’ /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:630:23: required from ‘void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::IT92]’ /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:726:44: required from here /<>/gemmi-0.5.1+ds/include/gemmi/formfact.hpp:27:24: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 27 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::impl::parse_cid(const string&, gemmi::Selection&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Bond&}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Torsion&}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/model.hpp:8, from /<>/gemmi-0.5.1+ds/src/rmsz.cpp:7: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::ChemMod::apply_to(gemmi::ChemComp&) const’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/ostream:38, from /usr/include/c++/11/iostream:39, from /<>/gemmi-0.5.1+ds/src/rmsz.cpp:5: /usr/include/c++/11/bits/stl_algobase.h:2114:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2114 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2115 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:66, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/model.hpp:8, from /<>/gemmi-0.5.1+ds/src/rmsz.cpp:7: /usr/include/c++/11/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gemmi::Restraints::Plane*; bool _TrivialValueTypes = false]’: /usr/include/c++/11/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 85 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_uninitialized.h: In copy constructor ‘gemmi::Restraints::Restraints(const gemmi::Restraints&)’: /usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 148 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 151 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object CMakeFiles/program.dir/src/sg.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/sg.cpp /usr/include/c++/11/bits/stl_uninitialized.h: In member function ‘void gemmi::Topo::initialize_refmac_topology(const gemmi::Structure&, gemmi::Model&, gemmi::MonLib&, bool)’: /usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 148 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 151 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/ccp4.hpp:16, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:7: /usr/include/c++/11/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const double*; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:721:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 721 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object CMakeFiles/program.dir/src/tags.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/tags.cpp [ 95%] Building CXX object CMakeFiles/program.dir/src/validate.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/validate.cpp /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::SmallStructure::Site&}; _Tp = gemmi::SmallStructure::Site; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::SmallStructure::AtomType&}; _Tp = gemmi::SmallStructure::AtomType; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/ccp4.hpp:16, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:7: /usr/include/c++/11/bits/stl_vector.h: In function ‘gemmi::SmallStructure gemmi::make_small_structure_from_block(const gemmi::cif::Block&)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/ccp4.hpp:16, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/ccp4.hpp:16, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:7: /usr/include/c++/11/bits/stl_vector.h: In member function ‘std::complex gemmi::StructureFactorCalculator::calculate_sf_from_model(const gemmi::Model&, const Miller&) [with Table = gemmi::C4322]’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_model(const gemmi::Model&, const Miller&) [with Table = gemmi::IT92]’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const Miller&) [with Table = gemmi::IT92]’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const Miller&) [with Table = gemmi::C4322]’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/ccp4.hpp:16, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:7: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Scaling::Point}; _Tp = gemmi::Scaling::Point; _Alloc = std::allocator::Point>]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::Point, std::allocator::Point> >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::Point, std::allocator::Point> >::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::Scaling::prepare_points(const gemmi::AsuData >&, const gemmi::AsuData >&, const gemmi::AsuData >&) [with Real = float]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator::Point*, std::vector::Point, std::allocator::Point> > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/ccp4.hpp:16, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:7: /usr/include/c++/11/bits/stl_vector.h: In member function ‘std::vector gemmi::Scaling::get_parameters() const [with Real = float]’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1313:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1313 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1314 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1313:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1313 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1314 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1313:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1313 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1314 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1313:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1313 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1314 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1313:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1313 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1314 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1313:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1313 | _M_range_insert(begin() + __offset, __l.begin(), __l.end(), | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1314 | std::random_access_iterator_tag()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/tao/pegtl/parse_error.hpp:8, from /usr/include/tao/pegtl/normal.hpp:13, from /usr/include/tao/pegtl/parse.hpp:11, from /usr/include/tao/pegtl.hpp:10, from /<>/gemmi-0.5.1+ds/include/gemmi/cif.hpp:13, from /<>/gemmi-0.5.1+ds/src/validate.cpp:3: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘{anonymous}::Validator2::Validator2(gemmi::cif::Block&, const std::map, std::__cxx11::basic_regex >&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Building CXX object CMakeFiles/program.dir/src/validate_mon.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/validate_mon.cpp /usr/include/c++/11/bits/stl_vector.h: In function ‘void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::IT92]’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In function ‘void {anonymous}::process(const string&, const OptParser&)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/iterator.hpp:9, from /<>/gemmi-0.5.1+ds/include/gemmi/cifdoc.hpp:8, from /<>/gemmi-0.5.1+ds/src/validate_mon.cpp:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 [ 97%] Building CXX object CMakeFiles/program.dir/src/wcn.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/src/wcn.cpp /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In function ‘gemmi::ChemComp gemmi::make_chemcomp_from_block(const gemmi::cif::Block&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/neighbor.hpp:9, from /<>/gemmi-0.5.1+ds/src/wcn.cpp:5: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Transform&}; _Tp = gemmi::Transform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/neighbor.hpp:9, from /<>/gemmi-0.5.1+ds/src/wcn.cpp:5: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void gemmi::NeighborSearch::initialize(gemmi::Model&, const gemmi::UnitCell&, double)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /<>/gemmi-0.5.1+ds/include/gemmi/neighbor.hpp:9, from /<>/gemmi-0.5.1+ds/src/wcn.cpp:5: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘int wcn_main(int, char**)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /<>/gemmi-0.5.1+ds/include/gemmi/neighbor.hpp:9, from /<>/gemmi-0.5.1+ds/src/wcn.cpp:5: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [100%] Linking CXX executable gemmi /usr/bin/cmake -E cmake_link_script CMakeFiles/program.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/program.dir/src/align.cpp.o CMakeFiles/program.dir/src/blobs.cpp.o CMakeFiles/program.dir/src/cif2mtz.cpp.o CMakeFiles/program.dir/src/cif2json.cpp.o CMakeFiles/program.dir/src/contact.cpp.o CMakeFiles/program.dir/src/contents.cpp.o CMakeFiles/program.dir/src/convert.cpp.o CMakeFiles/program.dir/src/fprime.cpp.o CMakeFiles/program.dir/src/grep.cpp.o CMakeFiles/program.dir/src/h.cpp.o CMakeFiles/program.dir/src/json2cif.cpp.o CMakeFiles/program.dir/src/main.cpp.o CMakeFiles/program.dir/src/map.cpp.o CMakeFiles/program.dir/src/map2sf.cpp.o CMakeFiles/program.dir/src/mask.cpp.o CMakeFiles/program.dir/src/merge.cpp.o CMakeFiles/program.dir/src/mondiff.cpp.o CMakeFiles/program.dir/src/mtz.cpp.o CMakeFiles/program.dir/src/mtz2cif.cpp.o CMakeFiles/program.dir/src/reindex.cpp.o CMakeFiles/program.dir/src/residues.cpp.o CMakeFiles/program.dir/src/rmsz.cpp.o CMakeFiles/program.dir/src/sf2map.cpp.o CMakeFiles/program.dir/src/sfcalc.cpp.o CMakeFiles/program.dir/src/sg.cpp.o CMakeFiles/program.dir/src/tags.cpp.o CMakeFiles/program.dir/src/validate.cpp.o CMakeFiles/program.dir/src/validate_mon.cpp.o CMakeFiles/program.dir/src/wcn.cpp.o CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o CMakeFiles/input.dir/src/input.cpp.o CMakeFiles/output.dir/src/output.cpp.o CMakeFiles/options.dir/src/options.cpp.o -o gemmi /usr/lib/arm-linux-gnueabihf/libz.so make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [100%] Built target program /usr/include/pybind11/pybind11.h: In member function ‘operator()’: /usr/include/pybind11/pybind11.h:190:21: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 190 | rec->impl = [](function_call &call) -> handle { | ^ ./include/gemmi/dencalc.hpp: In member function ‘calculate_with_derivative’: ./include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /usr/bin/strip /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/gemmi.cpython-39-arm-linux-gnueabihf.so make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [100%] Built target py make[2]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/gemmi-0.5.1+ds' dh_auto_build -- check cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" check VERBOSE=1 make[2]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<>/gemmi-0.5.1+ds -B/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<>/gemmi-0.5.1+ds -B/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles 41 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/depend make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/depend make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf 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[ 2%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/examples/check_conn.cpp make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[5]: Nothing to be done for 'CMakeFiles/input.dir/build'. make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 4%] Built target output Consolidate compiler generated dependencies of target mapcoef make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/options.dir/DependInfo.cmake --color= make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[5]: Nothing to be done for 'CMakeFiles/mapcoef.dir/build'. make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 4%] Built target input make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/depend make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/cpptest.dir/DependInfo.cmake --color= Dependencies file "CMakeFiles/options.dir/src/options.cpp.o.d" is newer than depends file "/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/options.dir/compiler_depend.internal". [ 7%] Built target mapcoef make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend Consolidate compiler generated dependencies of target options make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/hello.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[5]: Nothing to be done for 'CMakeFiles/options.dir/build'. make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 9%] Built target options make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/depend make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' cd /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf /<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf/CMakeFiles/doc_example.dir/DependInfo.cmake --color= [ 12%] Building CXX object CMakeFiles/cpptest.dir/tests/main.cpp.o make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/tests/main.cpp make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/build make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 14%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/examples/hello.cpp [ 14%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/docs/code/sym.cpp In file included from /<>/gemmi-0.5.1+ds/tests/main.cpp:3: /<>/gemmi-0.5.1+ds/third_party/doctest.h:4041:47: error: size of array ‘altStackMem’ is not an integral constant-expression 4041 | static char altStackMem[4 * SIGSTKSZ]; | ^ make[5]: *** [CMakeFiles/cpptest.dir/build.make:79: CMakeFiles/cpptest.dir/tests/main.cpp.o] Error 1 make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[4]: *** [CMakeFiles/Makefile2:1052: CMakeFiles/cpptest.dir/all] Error 2 make[4]: *** Waiting for unfinished jobs.... [ 17%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/docs/code/elem.cpp [ 19%] Building CXX object CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/docs/code/resinfo.cpp [ 19%] Building CXX object CMakeFiles/doc_example.dir/docs/code/cell.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+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 /<>/gemmi-0.5.1+ds/docs/code/cell.cpp [ 21%] 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=/<>/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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 '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 21%] Built target doc_example [ 24%] 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=/<>/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic CMakeFiles/hello.dir/examples/hello.cpp.o -o hello make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 24%] Built target hello In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/fileutil.hpp:16, from /<>/gemmi-0.5.1+ds/include/gemmi/gz.hpp:14, from /<>/gemmi-0.5.1+ds/examples/check_conn.cpp:5: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Mat33, gemmi::Vec3}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gemmi::Assembly::Operator&}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In function ‘std::vector gemmi::impl::read_assemblies(gemmi::cif::Block&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/fileutil.hpp:16, from /<>/gemmi-0.5.1+ds/include/gemmi/gz.hpp:14, from /<>/gemmi-0.5.1+ds/examples/check_conn.cpp:5: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from /usr/include/c++/11/functional:62, from /usr/include/c++/11/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/11/algorithm:74, from /<>/gemmi-0.5.1+ds/include/gemmi/util.hpp:8, from /<>/gemmi-0.5.1+ds/include/gemmi/fileutil.hpp:16, from /<>/gemmi-0.5.1+ds/include/gemmi/gz.hpp:14, from /<>/gemmi-0.5.1+ds/examples/check_conn.cpp:5: /usr/include/c++/11/bits/vector.tcc: In function ‘void gemmi::impl::read_connectivity(gemmi::cif::Block&, gemmi::Structure&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘gemmi::Structure gemmi::impl::make_structure_from_block(const gemmi::cif::Block&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 24%] 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=/<>/gemmi-0.5.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -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 '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' [ 24%] Built target check_conn make[4]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[3]: *** [CMakeFiles/Makefile2:1327: CMakeFiles/check.dir/rule] Error 2 make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' make[2]: *** [Makefile:754: check] Error 2 make[2]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-arm-linux-gnueabihf' dh_auto_build: error: cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" check VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:14: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<>/gemmi-0.5.1+ds' make: *** [debian/rules:8: binary-arch] Error 2 dpkg-buildpackage.pl: error: debian/rules binary-arch subprocess returned exit status 2 === USAGE-SUMMARY BEGIN === SUMMARY: host: bos02-arm64-071; CPUs: 4/4; CPU avg: 62%; CPU max: 100%; base memory: 0.2 GB; peak memory: 1.9 GB; total memory: 7.8 GB SUMMARY: swap peak/total: 0.0/0.0 GB; disk start/end/total: 2.3/2.9/77.4 GB; disk delta: 0.5 GB === USAGE-SUMMARY END === -------------------------------------------------------------------------------- Build finished at 2022-01-15T00:26:47Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: n/a Build-Time: 837 Distribution: jammy Fail-Stage: build Host Architecture: armhf Install-Time: 29 Job: gemmi_0.5.1+ds-1.dsc Machine Architecture: arm64 Package: gemmi Package-Time: 869 Source-Version: 0.5.1+ds-1 Space: n/a Status: attempted Version: 0.5.1+ds-1 -------------------------------------------------------------------------------- Finished at 2022-01-15T00:26:47Z Build needed 00:14:29, no disk space E: Build failure (dpkg-buildpackage died) Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22765110 Scanning for processes to kill in build PACKAGEBUILD-22765110