https://launchpad.net/ubuntu/+source/gemmi/0.6.4+ds-1build1/+build/27660667 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-041 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 aarch64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 19 Jan 19:24:41 ntpdate[1872]: adjust time server 10.211.37.1 offset -0.000501 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27660667 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-27660667 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27660667 Starting target for build PACKAGEBUILD-27660667 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27660667 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27660667 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27660667 Updating target for build PACKAGEBUILD-27660667 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1385 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.2 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6019 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [178 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [68.9 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [807 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [338 kB] Fetched 25.1 MB in 7s (3755 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-aarch64-linux-gnu binutils-common bsdextrautils bsdutils coreutils cpp cpp-13 debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base grep init init-system-helpers krb5-locales libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps psmisc readline-common sed systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring usrmerge util-linux uuid-runtime xz-utils zlib1g 149 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 116 MB of archives. After this operation, 56.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.38-3ubuntu1 [1573 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.38-3ubuntu1 [19.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgssapi-krb5-2 arm64 1.20.1-5build1 [139 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5-3 arm64 1.20.1-5build1 [347 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libk5crypto3 arm64 1.20.1-5build1 [85.5 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5support0 arm64 1.20.1-5build1 [33.5 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libssl3 arm64 3.0.10-1ubuntu3 [1752 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc3 arm64 1.3.4+ds-1build1 [99.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl2 arm64 1.3.0-3 [40.9 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcrypt1 arm64 1:4.4.36-4 [100 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.6.0-14.14 [1554 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcc1-0 arm64 13.2.0-10ubuntu1 [49.5 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgprofng0 arm64 2.41.90.20240115-1ubuntu1 [777 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libctf0 arm64 2.41.90.20240115-1ubuntu1 [95.8 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libctf-nobfd0 arm64 2.41.90.20240115-1ubuntu1 [99.5 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.41.90.20240115-1ubuntu1 [3296 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libbinutils arm64 2.41.90.20240115-1ubuntu1 [767 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 binutils-common arm64 2.41.90.20240115-1ubuntu1 [238 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 binutils arm64 2.41.90.20240115-1ubuntu1 [18.0 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-base arm64 13.2.0-10ubuntu1 [46.2 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-s1 arm64 13.2.0-10ubuntu1 [46.6 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgomp1 arm64 13.2.0-10ubuntu1 [139 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libitm1 arm64 13.2.0-10ubuntu1 [27.9 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libatomic1 arm64 13.2.0-10ubuntu1 [11.6 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libasan8 arm64 13.2.0-10ubuntu1 [2742 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblsan0 arm64 13.2.0-10ubuntu1 [1185 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtsan2 arm64 13.2.0-10ubuntu1 [2630 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libubsan1 arm64 13.2.0-10ubuntu1 [1090 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhwasan0 arm64 13.2.0-10ubuntu1 [1243 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13 arm64 13.2.0-10ubuntu1 [10.9 MB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++-13-dev arm64 13.2.0-10ubuntu1 [2319 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-13-dev arm64 13.2.0-10ubuntu1 [2463 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13 arm64 13.2.0-10ubuntu1 [19.1 MB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13 arm64 13.2.0-10ubuntu1 [9536 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++6 arm64 13.2.0-10ubuntu1 [732 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g arm64 1:1.3.dfsg-3ubuntu1 [61.6 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsframe1 arm64 2.41.90.20240115-1ubuntu1 [14.1 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2 [270 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libc6 arm64 2.38-3ubuntu1 [2740 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 base-files arm64 13ubuntu6 [84.1 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 debianutils arm64 5.16 [93.7 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 bash arm64 5.2.21-2ubuntu1 [777 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 bsdutils arm64 1:2.39.2-6ubuntu1 [96.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 coreutils arm64 9.4-2ubuntu2 [1715 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1 [174 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build1 [69.9 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcrypt20 arm64 1.10.3-2 [472 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma5 arm64 5.4.5-0.3 [140 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.1-4ubuntu1 [19.4 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libapparmor1 arm64 4.0.0~alpha2-0ubuntu7 [48.7 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit-common all 1:3.1.2-1 [5512 B] Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libcap-ng0 arm64 0.8.4-1 [16.4 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit1 arm64 1:3.1.2-1 [47.0 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libblkid1 arm64 2.39.2-6ubuntu1 [121 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libkmod2 arm64 30+20230601-2ubuntu1 [49.8 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu1 [211 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libselinux1 arm64 3.5-1build2 [78.4 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libmount1 arm64 2.39.2-6ubuntu1 [132 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-iconv-perl arm64 1.7-8build1 [13.0 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-charwidth-perl arm64 0.04-11build1 [9316 B] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38 arm64 5.38.2-3 [4772 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3 [231 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3 [1777 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblocale-gettext-perl arm64 1.07-6build1 [15.0 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libperl5.36 arm64 5.36.0-10ubuntu1 [4673 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libdb5.3 arm64 5.3.28+dfsg2-4 [718 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm6 arm64 1.23-5 [33.8 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm-compat4 arm64 1.23-5 [6302 B] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debconf-i18n all 1.5.83 [238 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debconf all 1.5.83 [147 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam0g arm64 1.5.2-9.1ubuntu2 [65.8 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libseccomp2 arm64 2.5.4-2ubuntu1 [50.1 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-sysv arm64 255.2-3ubuntu1 [12.5 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-dev all 255.2-3ubuntu1 [107 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd arm64 255.2-3ubuntu1 [3944 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd-shared arm64 255.2-3ubuntu1 [2452 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4 [20.5 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libuuid1 arm64 2.39.2-6ubuntu1 [34.3 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libcryptsetup12 arm64 2:2.6.1-6ubuntu1 [240 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libfdisk1 arm64 2.39.2-6ubuntu1 [141 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 mount arm64 2.39.2-6ubuntu1 [116 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd0 arm64 255.2-3ubuntu1 [489 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libudev1 arm64 255.2-3ubuntu1 [187 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2 [21.2 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapt-pkg6.0 arm64 2.7.10 [929 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3 [248 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg arm64 1.22.2ubuntu2 [1290 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4 [174 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-3ubuntu1 [200 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ncurses-bin arm64 6.4+20240113-1 [186 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2 [201 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 util-linux arm64 2.39.2-6ubuntu1 [1113 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libdebconfclient0 arm64 0.271ubuntu1 [11.2 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3 [51.1 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libc-bin arm64 2.38-3ubuntu1 [590 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ncurses-base all 6.4+20240113-1 [25.4 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-3ubuntu1 [33.3 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt arm64 2.7.10 [1333 kB] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt-utils arm64 2.7.10 [205 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.4-2 [22.2 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-2ubuntu2 [274 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2 [528 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.4-1build1 [65.3 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30 arm64 3.8.1-4ubuntu7 [938 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-modules-bin arm64 1.5.2-9.1ubuntu2 [47.0 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-modules arm64 1.5.2-9.1ubuntu2 [284 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 libsmartcols1 arm64 2.39.2-6ubuntu1 [62.9 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 uuid-runtime arm64 2.39.2-6ubuntu1 [32.3 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.1-5 [12.7 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2 [24.7 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage-common all 3.5-1build1 [9982 B] Get:123 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2 [289 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage2 arm64 3.5-1build1 [90.0 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libncursesw6 arm64 6.4+20240113-1 [145 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtinfo6 arm64 6.4+20240113-1 [104 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-3ubuntu1 [837 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-2ubuntu1 [56.5 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20231126-1 [123 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-2ubuntu1 [706 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main arm64 usrmerge all 38ubuntu1 [58.8 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main arm64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 readline-common all 8.2-3 [56.2 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline8 arm64 8.2-3 [152 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 libsqlite3-0 arm64 3.44.2-1 [691 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 openssl arm64 3.0.10-1ubuntu3 [1168 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2023d-1ubuntu2 [321 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main arm64 bsdextrautils arm64 2.39.2-6ubuntu1 [71.4 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main arm64 libpng16-16 arm64 1.6.40-3 [203 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 psmisc arm64 23.6-2 [178 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 xz-utils arm64 5.4.5-0.3 [277 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-2ubuntu1 [1108 B] Get:144 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-2ubuntu1 [5192 B] Get:145 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-2ubuntu1 [29.0 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 dpkg-dev all 1.22.2ubuntu2 [1168 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 libdpkg-perl all 1.22.2ubuntu2 [321 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 45 [12.4 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 libfakeroot arm64 1.32.2-1 [32.0 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 fakeroot arm64 1.32.2-1 [66.7 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 optipng arm64 0.7.7-3 [82.1 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 pinentry-curses arm64 1.2.1-3ubuntu1 [34.0 kB] Preconfiguring packages ... 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Setting up binutils (2.41.90.20240115-1ubuntu1) ... Setting up perl (5.38.2-3) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1build1) ... Setting up gcc-13 (13.2.0-10ubuntu1) ... Setting up libdpkg-perl (1.22.2ubuntu2) ... Setting up libnsl2:arm64 (1.3.0-3) ... Setting up gcc (4:13.2.0-2ubuntu1) ... Setting up dpkg-dev (1.22.2ubuntu2) ... Setting up libnsl-dev:arm64 (1.3.0-3) ... Setting up libc6-dev:arm64 (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:arm64 (13.2.0-10ubuntu1) ... Setting up g++-13 (13.2.0-10ubuntu1) ... Setting up g++ (4:13.2.0-2ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for debianutils (5.16) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27660667 arm64 noble-proposed -c chroot:build-PACKAGEBUILD-27660667 --arch=arm64 --dist=noble-proposed --nolog gemmi_0.6.4+ds-1build1.dsc Initiating build PACKAGEBUILD-27660667 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-041.buildd +==============================================================================+ | gemmi 0.6.4+ds-1build1 (arm64) Fri, 19 Jan 2024 19:25:56 +0000 | +==============================================================================+ Package: gemmi Version: 0.6.4+ds-1build1 Source Version: 0.6.4+ds-1build1 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27660667/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/gemmi-DGiU04/resolver-eRcoo6' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gemmi_0.6.4+ds-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/gemmi-DGiU04/gemmi-0.6.4+ds' with '<>' I: NOTICE: Log filtering will replace 'build/gemmi-DGiU04' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), dh-python, doctest-dev, help2man, libstb-dev, python3-dev, python3-numpy, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: cmake, debhelper-compat (= 13), dh-python, doctest-dev, help2man, libstb-dev, python3-dev, python3-numpy, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [452 B] Get:5 copy:/<>/apt_archive ./ Packages [526 B] Fetched 1935 B in 0s (64.0 kB/s) Reading package lists... Reading package lists... Install main 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: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism doctest-dev dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libblas3 libbrotli1 libcurl4 libdebhelper-perl libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libicu74 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp25 liblapack3 libldap2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython3-dev libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libstb-dev libstb0 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db media-types netbase po-debconf pybind11-dev python3 python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-pybind11 python3-pytest python3-setuptools python3.11 python3.11-minimal python3.12 python3.12-dev python3.12-minimal tao-pegtl-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flit python3-build python3-installer python3-wheel 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 python3-doc python3-tk python3-venv gfortran python-setuptools-doc python3.11-venv python3.11-doc binfmt-support python3.12-venv python3.12-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl libeigen3-dev python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism doctest-dev dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libblas3 libbrotli1 libcurl4 libdebhelper-perl libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libicu74 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp25 liblapack3 libldap2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython3-dev libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libstb-dev libstb0 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db media-types netbase po-debconf pybind11-dev python3 python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-pybind11 python3-pytest python3-setuptools python3.11 python3.11-minimal python3.12 python3.12-dev python3.12-minimal sbuild-build-depends-main-dummy tao-pegtl-dev zlib1g-dev 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. 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Fetched 68.3 MB in 12s (5744 kB/s) Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... 15802 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.1-2_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.1-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-2_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.1-2_arm64.deb ... Unpacking python3.12-minimal (3.12.1-2) ... Setting up libpython3.12-minimal:arm64 (3.12.1-2) ... Setting up libexpat1:arm64 (2.5.0-2) ... Setting up python3.12-minimal (3.12.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 16120 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu1_arm64.deb ... 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Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.12.1-0ubuntu1) ... Setting up libpython3.12-dev:arm64 (3.12.1-2) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up python3-packaging (23.2-1) ... Setting up python3.12-dev (3.12.1-2) ... Setting up python3-pluggy (1.3.0-1) ... Setting up cmake (3.28.1-1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-iniconfig (1.1.1-2) ... Setting up libpython3-dev:arm64 (3.12.1-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-pytest (7.4.4-1) ... Setting up debhelper (13.11.9ubuntu1) ... Setting up pybind11-dev (2.11.1-2) ... Setting up python3-dev (3.12.1-0ubuntu1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-pybind11 (2.11.1-2) ... Setting up dh-python (6.20231223) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (255.2-3ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 arm64 (aarch64) Toolchain package versions: binutils_2.41.90.20240115-1ubuntu1 dpkg-dev_1.22.2ubuntu2 g++-13_13.2.0-10ubuntu1 gcc-13_13.2.0-10ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-10ubuntu1 libstdc++6_13.2.0-10ubuntu1 linux-libc-dev_6.6.0-14.14 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.10 apt-utils_2.7.10 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13ubuntu6 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.41.90.20240115-1ubuntu1 binutils-aarch64-linux-gnu_2.41.90.20240115-1ubuntu1 binutils-common_2.41.90.20240115-1ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 cmake_3.28.1-1 cmake-data_3.28.1-1 coreutils_9.4-2ubuntu2 cpp_4:13.2.0-2ubuntu1 cpp-13_13.2.0-10ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.83 debconf-i18n_1.5.83 debhelper_13.11.9ubuntu1 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_6.20231223 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 doctest-dev_2.4.11-1 dpkg_1.22.2ubuntu2 dpkg-dev_1.22.2ubuntu2 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-2ubuntu1 g++-13_13.2.0-10ubuntu1 gcc_4:13.2.0-2ubuntu1 gcc-13_13.2.0-10ubuntu1 gcc-13-base_13.2.0-10ubuntu1 gettext_0.21-14 gettext-base_0.21-14 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 help2man_1.49.3 hostname_3.23+nmu1ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5build1 libacl1_2.3.1-4ubuntu1 libapparmor1_4.0.0~alpha2-0ubuntu7 libapt-pkg6.0_2.7.10 libarchive-zip-perl_1.68-1 libarchive13_3.7.2-1ubuntu2 libargon2-1_0~20190702+dfsg-4 libasan8_13.2.0-10ubuntu1 libassuan0_2.5.6-1 libatomic1_13.2.0-10ubuntu1 libattr1_1:2.5.1-5 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41.90.20240115-1ubuntu1 libblas3_3.11.0-2build1 libblkid1_2.39.2-6ubuntu1 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-3ubuntu1 libc-dev-bin_2.38-3ubuntu1 libc6_2.38-3ubuntu1 libc6-dev_2.38-3ubuntu1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4ubuntu1 libcc1-0_13.2.0-10ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.6.1-6ubuntu1 libctf-nobfd0_2.41.90.20240115-1ubuntu1 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-o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -c /<>/src/calculate.cpp In file included from /<>/prog/options.cpp:8: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -c /<>/src/crd.cpp [ 8%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -c /<>/src/ddl.cpp make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 8%] Built target options [ 8%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -c /<>/src/eig3.cpp [ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /<>/src/mmcif.cpp [ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -c /<>/src/mmread_gz.cpp In file included from /<>/include/gemmi/json.hpp:19, from /<>/include/gemmi/mmread.hpp:12, from /<>/src/mmread_gz.cpp:4: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 13%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o -c /<>/src/mtz.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/src/mtz.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 15%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -c /<>/src/mtz2cif.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/mtz2cif.hpp:14, from /<>/src/mtz2cif.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 15%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -c /<>/src/polyheur.cpp [ 17%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -c /<>/src/read_cif.cpp [ 17%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -c /<>/src/resinfo.cpp [ 19%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -c /<>/src/riding_h.cpp In file included from /<>/include/gemmi/json.hpp:19, from /<>/src/read_cif.cpp:5: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 19%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -c /<>/src/sprintf.cpp /<>/src/sprintf.cpp:30:86: note: ‘#pragma message: Using system stb_sprintf.h, not the bundled one. It may not work.’ 30 | # pragma message("Using system stb_sprintf.h, not the bundled one. It may not work.") | ^ [ 21%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /<>/src/to_mmcif.cpp [ 23%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -c /<>/src/to_pdb.cpp [ 23%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /<>/src/monlib.cpp [ 26%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -c /<>/src/topo.cpp [ 26%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -c /<>/src/xds_ascii.cpp In file included from /<>/include/gemmi/xds_ascii.hpp:11, from /<>/src/xds_ascii.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /usr/include/c++/13/bits/stl_tree.h:63, from /usr/include/c++/13/map:62, from /<>/include/gemmi/topo.hpp:8, from /<>/src/topo.cpp:3: In function ‘std::__copy_move::__copy_m(gemmi::Topo::Rule*, gemmi::Topo::Rule*, gemmi::Topo::Rule*)gemmi::Topo::Rule*’, inlined from ‘std::__copy_move_a2(gemmi::Topo::Rule*, gemmi::Topo::Rule*, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_algobase.h:506:30, inlined from ‘std::__copy_move_a1(gemmi::Topo::Rule*, gemmi::Topo::Rule*, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_algobase.h:533:42, inlined from ‘std::__copy_move_a > >, gemmi::Topo::Rule*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_algobase.h:540:31, inlined from ‘std::copy > > >, gemmi::Topo::Rule*>(std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_algobase.h:633:7, inlined from ‘std::__uninitialized_copy::__uninit_copy > > >, gemmi::Topo::Rule*>(std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_uninitialized.h:147:27, inlined from ‘std::uninitialized_copy > > >, gemmi::Topo::Rule*>(std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, gemmi::Topo::Rule*)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from ‘std::__uninitialized_copy_a > > >, gemmi::Topo::Rule*, gemmi::Topo::Rule>(std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, gemmi::Topo::Rule*, std::allocator&)gemmi::Topo::Rule*’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, inlined from ‘std::vector >::_M_range_insert > > > >(__gnu_cxx::__normal_iterator > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::forward_iterator_tag)void’ at /usr/include/c++/13/bits/vector.tcc:814:38, inlined from ‘std::vector >::insert > > >, void>(__gnu_cxx::__normal_iterator > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >)__gnu_cxx::__normal_iterator > >’ at /usr/include/c++/13/bits/stl_vector.h:1483:19, inlined from ‘gemmi::vector_move_extend(std::vector >&, std::vector >&&)void’ at /<>/include/gemmi/util.hpp:260:15, inlined from ‘gemmi::Topo::apply_all_restraints(gemmi::MonLib const&)’ at /<>/src/topo.cpp:594:27: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: ‘memmove’ writing between 17 and 9223372036854775792 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/aarch64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/stl_tree.h:64: In member function ‘std::__new_allocator::allocate(unsigned long, void const*)’, inlined from ‘std::allocator_traits >::allocate(std::allocator&, unsigned long)’ at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from ‘std::_Vector_base >::_M_allocate(unsigned long)’ at /usr/include/c++/13/bits/stl_vector.h:378:33, inlined from ‘std::_Vector_base >::_M_allocate(unsigned long)’ at /usr/include/c++/13/bits/stl_vector.h:375:7, inlined from ‘std::vector >::_M_range_insert > > > >(__gnu_cxx::__normal_iterator > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::forward_iterator_tag)void’ at /usr/include/c++/13/bits/vector.tcc:805:40, inlined from ‘std::vector >::insert > > >, void>(__gnu_cxx::__normal_iterator > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >, std::move_iterator<__gnu_cxx::__normal_iterator > > >)__gnu_cxx::__normal_iterator > >’ at /usr/include/c++/13/bits/stl_vector.h:1483:19, inlined from ‘gemmi::vector_move_extend(std::vector >&, std::vector >&&)void’ at /<>/include/gemmi/util.hpp:260:15, inlined from ‘gemmi::Topo::apply_all_restraints(gemmi::MonLib const&)’ at /<>/src/topo.cpp:594:27: /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [16, 9223372036854775792] allocated by ‘operator new(unsigned long)’ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 28%] Linking CXX static library libgemmi_cpp.a /usr/bin/cmake -P CMakeFiles/gemmi_cpp.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libgemmi_cpp.a CMakeFiles/gemmi_cpp.dir/src/align.cpp.o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/bin/ranlib libgemmi_cpp.a make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 28%] Built target gemmi_cpp make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/depend make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/gemmi_py.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 32%] Building CXX object CMakeFiles/gemmi_py.dir/python/align.cpp.o [ 32%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o [ 32%] Building CXX object CMakeFiles/gemmi_py.dir/python/mol.cpp.o [ 32%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/align.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/align.cpp.o -MF CMakeFiles/gemmi_py.dir/python/align.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/align.cpp.o -c /<>/python/align.cpp /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 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/<>/python/gemmi.cpp [ 32%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -MF CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -c /<>/python/ccp4.cpp [ 34%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -c /<>/prog/blobs.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/python/ccp4.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 36%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -MF CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -c /<>/python/chemcomp.cpp [ 39%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -c /<>/prog/cif2mtz.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/cif2mtz.hpp:15, from /<>/prog/cif2mtz.cpp:10: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 39%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time 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/usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mtz.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -c /<>/python/mtz.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/python/mtz.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 52%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -c /<>/prog/convert.cpp [ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/read.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/read.cpp.o -MF CMakeFiles/gemmi_py.dir/python/read.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/read.cpp.o -c /<>/python/read.cpp In file included from /<>/include/gemmi/pdb.hpp:23, from /<>/python/read.cpp:7: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 54%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/diff.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/diff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/diff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/diff.cpp.o -c /<>/prog/diff.cpp [ 56%] Building CXX object CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -c /<>/python/recgrid.cpp [ 58%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -c /<>/prog/ecalc.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/ecalc.cpp:5: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 58%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -c /<>/prog/fprime.cpp [ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -c /<>/prog/grep.cpp In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/grep.cpp:6: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 63%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/h.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/h.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -c /<>/prog/h.cpp [ 63%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -c /<>/prog/json2cif.cpp [ 63%] Building CXX object CMakeFiles/gemmi_py.dir/python/scaling.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -MF CMakeFiles/gemmi_py.dir/python/scaling.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -c /<>/python/scaling.cpp [ 65%] Building CXX object CMakeFiles/gemmi_py.dir/python/search.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/search.cpp.o -MF CMakeFiles/gemmi_py.dir/python/search.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/search.cpp.o -c /<>/python/search.cpp [ 67%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/main.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/main.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -c /<>/prog/main.cpp [ 67%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -c /<>/prog/map.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/prog/map.cpp:6: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 69%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -c /<>/prog/map2sf.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/map2sf.cpp:10: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 69%] Building CXX object CMakeFiles/gemmi_py.dir/python/sf.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sf.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sf.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sf.cpp.o -c /<>/python/sf.cpp [ 69%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -c /<>/prog/mapcoef.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/mapcoef.cpp:11: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /<>/include/gemmi/it92.hpp:16, from /<>/python/sf.cpp:6: /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]’ /<>/python/sf.cpp:60:36: required from ‘void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]’ /<>/python/sf.cpp:83:20: required from here /<>/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 73 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]’ /<>/python/sf.cpp:60:36: required from ‘void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::Neutron92; pybind11::module = pybind11::module_]’ /<>/python/sf.cpp:85:25: required from here /<>/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 48 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 1]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = float]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]’ /<>/include/gemmi/dencalc.hpp:149:37: required from ‘void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, float>; Table = gemmi::IT92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:128:32: required from ‘void gemmi::DensityCalculator::add_c_contribution_to_grid(const gemmi::Atom&, float) [with Table = gemmi::IT92; GReal = float]’ /<>/python/sf.cpp:47:40: required from ‘void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]’ /<>/python/sf.cpp:83:20: required from here /<>/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 73 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 71%] Building CXX object CMakeFiles/gemmi_py.dir/python/sym.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sym.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sym.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sym.cpp.o -c /<>/python/sym.cpp [ 73%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -c /<>/prog/mask.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/prog/mask.cpp:5: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 73%] Building CXX object CMakeFiles/gemmi_py.dir/python/topo.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/topo.cpp.o -MF CMakeFiles/gemmi_py.dir/python/topo.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/topo.cpp.o -c /<>/python/topo.cpp [ 76%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -c /<>/prog/merge.cpp [ 76%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -c /<>/prog/mondiff.cpp In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/merge.cpp:11: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 78%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -MF CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -c /<>/python/unitcell.cpp [ 80%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -c /<>/prog/monlib_opt.cpp [ 80%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -c /<>/prog/mtz.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/mtz.cpp:8: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 82%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -c /<>/prog/mtz2cif.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/mtz2cif.hpp:14, from /<>/prog/mtz2cif.cpp:8: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 84%] Building CXX object CMakeFiles/gemmi_py.dir/python/write.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/<>/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/write.cpp.o -MF CMakeFiles/gemmi_py.dir/python/write.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/write.cpp.o -c /<>/python/write.cpp [ 84%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/prep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/prep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/prep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/prep.cpp.o -c /<>/prog/prep.cpp [ 86%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -c /<>/prog/reindex.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/prog/reindex.cpp:9: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 86%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -c /<>/prog/residues.cpp [ 86%] Linking CXX shared module gemmi.cpython-312-aarch64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_py.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -shared -o gemmi.cpython-312-aarch64-linux-gnu.so CMakeFiles/gemmi_py.dir/python/mol.cpp.o CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o CMakeFiles/gemmi_py.dir/python/align.cpp.o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o CMakeFiles/gemmi_py.dir/python/cif.cpp.o CMakeFiles/gemmi_py.dir/python/custom.cpp.o CMakeFiles/gemmi_py.dir/python/elem.cpp.o CMakeFiles/gemmi_py.dir/python/grid.cpp.o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o CMakeFiles/gemmi_py.dir/python/meta.cpp.o CMakeFiles/gemmi_py.dir/python/monlib.cpp.o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o CMakeFiles/gemmi_py.dir/python/read.cpp.o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o CMakeFiles/gemmi_py.dir/python/search.cpp.o CMakeFiles/gemmi_py.dir/python/sf.cpp.o CMakeFiles/gemmi_py.dir/python/sym.cpp.o CMakeFiles/gemmi_py.dir/python/topo.cpp.o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o CMakeFiles/gemmi_py.dir/python/write.cpp.o CMakeFiles/gemmi_cpp.dir/src/align.cpp.o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/lib/aarch64-linux-gnu/libz.so [ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -c /<>/prog/rmsz.cpp [ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -c /<>/prog/sf2map.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/prog/sf2map.cpp:6: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -c /<>/prog/sfcalc.cpp [ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -c /<>/prog/sg.cpp In file included from /<>/include/gemmi/ccp4.hpp:19, from /<>/prog/sfcalc.cpp:9: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /<>/include/gemmi/it92.hpp:16, from /<>/prog/sfcalc.cpp:14: /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]’ /<>/include/gemmi/dencalc.hpp:149:37: required from ‘void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<4, 1, float>; Table = gemmi::IT92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:122:32: required from ‘void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::IT92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:196:11: required from ‘void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:201:5: required from ‘void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]’ /<>/prog/sfcalc.cpp:243:36: required from ‘void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::IT92; Real = float]’ /<>/prog/sfcalc.cpp:690:23: required from ‘void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::IT92]’ /<>/prog/sfcalc.cpp:812:43: required from here /<>/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 73 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/gemmi/formfact.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]’: /<>/include/gemmi/dencalc.hpp:19:54: required from ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]’ /<>/include/gemmi/dencalc.hpp:136:35: required from ‘gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]’ /<>/include/gemmi/dencalc.hpp:149:37: required from ‘void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, double>; Table = gemmi::Neutron92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:122:32: required from ‘void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::Neutron92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:196:11: required from ‘void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]’ /<>/include/gemmi/dencalc.hpp:201:5: required from ‘void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]’ /<>/prog/sfcalc.cpp:243:36: required from ‘void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::Neutron92; Real = float]’ /<>/prog/sfcalc.cpp:690:23: required from ‘void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::Neutron92]’ /<>/prog/sfcalc.cpp:817:49: required from here /<>/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 48 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/prog/sfcalc.cpp:19: /<>/include/gemmi/dencalc.hpp: In function ‘Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]’: /<>/include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -c /<>/prog/tags.cpp [ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -c /<>/prog/validate.cpp In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/tags.cpp:7: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/validate.cpp:5: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g 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-I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -c /<>/prog/wcn.cpp In file included from /<>/prog/wcn.cpp:10: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h: In member function ‘operator()’: /usr/lib/python3/dist-packages/pybind11/include/pybind11/pybind11.h:224: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 224 | rec->impl = [](function_call &call) -> handle { | [100%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -c /<>/prog/xds2mtz.cpp In file included from /<>/include/gemmi/gz.hpp:13, from /<>/prog/xds2mtz.cpp:7: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [100%] Linking CXX executable gemmi /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_prog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/gemmi_prog.dir/prog/align.cpp.o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o CMakeFiles/gemmi_prog.dir/prog/diff.cpp.o 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-mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -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 /<>/examples/check_conn.cpp [ 89%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF CMakeFiles/cpptest.dir/tests/cif.cpp.o.d -o CMakeFiles/cpptest.dir/tests/cif.cpp.o -c /<>/tests/cif.cpp In file included from /<>/include/gemmi/json.hpp:19, from /<>/include/gemmi/mmread.hpp:12, from /<>/tests/disulf.cpp:11: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/merge.hpp:15, from /<>/tests/cif.cpp:6: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 89%] Linking CXX executable doc_newmtz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so [ 91%] 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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 91%] Built target doc_newmtz make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/depend make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/doc_maybegz.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 91%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o /usr/bin/c++ -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /<>/docs/code/maybegz.cpp In file included from /<>/include/gemmi/json.hpp:19, from /<>/include/gemmi/mmread.hpp:12, from /<>/docs/code/maybegz.cpp:2: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 91%] Building CXX object CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o -MF CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o -c /<>/src/mtz2cif.cpp In file included from /<>/include/gemmi/mtz.hpp:23, from /<>/include/gemmi/mtz2cif.hpp:14, from /<>/src/mtz2cif.cpp:3: /<>/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument ‘int (*)(FILE*)’ [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 91%] Built target check_conn make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/depend make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/print-version.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/build make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 91%] gemmi --version cd /<> && /<>/obj-aarch64-linux-gnu/gemmi --version gemmi 0.6.4 make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 91%] Built target print-version [ 93%] Building CXX object CMakeFiles/cpptest.dir/src/eig3.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/src/eig3.cpp.o -MF CMakeFiles/cpptest.dir/src/eig3.cpp.o.d -o CMakeFiles/cpptest.dir/src/eig3.cpp.o -c /<>/src/eig3.cpp [ 95%] Building CXX object CMakeFiles/cpptest.dir/src/sprintf.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/<>/third_party -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/src/sprintf.cpp.o -MF CMakeFiles/cpptest.dir/src/sprintf.cpp.o.d -o CMakeFiles/cpptest.dir/src/sprintf.cpp.o -c /<>/src/sprintf.cpp [ 97%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o /usr/bin/c++ -I/<>/include -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /<>/docs/code/mutate.cpp [ 97%] Linking CXX executable cpptest /usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o CMakeFiles/cpptest.dir/src/mtz2cif.cpp.o CMakeFiles/cpptest.dir/src/eig3.cpp.o CMakeFiles/cpptest.dir/src/sprintf.cpp.o -o cpptest make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [ 97%] Built target cpptest [100%] Linking CXX executable test_disulf /usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so [100%] Linking CXX executable doc_maybegz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/gemmi-0.6.4+ds-1build1 -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target test_disulf make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target doc_maybegz make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/ctest -C None Test project /<>/obj-aarch64-linux-gnu Start 1: cpptest 1/1 Test #1: cpptest .......................... Passed 0.01 sec 100% tests passed, 0 tests failed out of 1 Total Test time (real) = 0.01 sec make[5]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' PYTHONPATH=$(find . -name 'obj-*') pytest-3 -k 'not test_sfcalc_' ........................................................................ [ 38%] ............................s.................s......sssssssssssssss.... [ 76%] ............................................ [100%] =========================== short test summary info ============================ SKIPPED [1] tests/test_mol.py:535: BioPython not installed. SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. SKIPPED [1] tests/test_prog.py:121: Program gemmi not found. SKIPPED [1] tests/test_prog.py:130: Program gemmi not found. SKIPPED [1] tests/test_prog.py:139: Program gemmi not found. SKIPPED [1] tests/test_prog.py:47: Program gemmi not found. SKIPPED [1] tests/test_prog.py:55: Program gemmi not found. SKIPPED [1] tests/test_prog.py:62: Program gemmi not found. SKIPPED [1] tests/test_prog.py:68: Program gemmi not found. SKIPPED [1] tests/test_prog.py:74: Program gemmi not found. SKIPPED [1] tests/test_prog.py:80: Program gemmi not found. SKIPPED [1] tests/test_seq.py:127: BioPython not installed. SKIPPED [1] tests/test_seq.py:132: BioPython not installed. SKIPPED [1] tests/test_seq.py:139: BioPython not installed. SKIPPED [1] tests/test_seq.py:146: BioPython not installed. SKIPPED [1] tests/test_seq.py:105: BioPython not installed. SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 171 passed, 17 skipped, 2 deselected in 2.50s make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=cmake dh_prep -a -O--buildsystem=cmake dh_auto_install -a -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j4 install DESTDIR=/<>/gemmi-0.6.4\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/bin/gemmi -- Installing: /<>/debian/tmp/usr/include/gemmi -- Installing: 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/<>/debian/tmp/usr/include/gemmi/to_pdb.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/to_mmcif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/neutron92.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/resinfo.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/linkhunt.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmcif_impl.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/cellred.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mtz2cif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/eig3.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/asudata.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/fprime.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmread_gz.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/contact.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/select.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/qcp.hpp -- Installing: 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Installing: /<>/debian/tmp/usr/include/gemmi/span.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/read_cif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/blob.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/grid.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/utf.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/cif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/align.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/enumstr.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/crd.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/asumask.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/seqalign.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/assembly.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmcif.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/floodfill.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/monlib.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/solmask.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/levmar.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/cifdoc.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/numb.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/seqtools.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/mmread.hpp -- Installing: /<>/debian/tmp/usr/include/gemmi/atox.hpp -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/libgemmi_cpp.a -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-targets.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-targets-none.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-config.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-config-version.cmake -- Installing: /<>/debian/tmp/usr/lib/python3/dist-packages/gemmi.cpython-312-aarch64-linux-gnu.so make[1]: Leaving directory '/<>/obj-aarch64-linux-gnu' dh_install -a -O--buildsystem=cmake dh_installdocs -a -O--buildsystem=cmake dh_installchangelogs -a -O--buildsystem=cmake debian/rules override_dh_installman make[1]: Entering directory '/<>' help2man 'tail -n +9 docs/gemmi-help.txt' \ --version-string 0.6.4+ds --name 'CLI for GEMMI library' \ --no-info --help-option '' > debian/gemmi.1 sed -i 's/.TH GEMMI-HELP.TXT/.TH gemmi/' debian/gemmi.1 sed -i 's/gemmi-help.txt/gemmi/' debian/gemmi.1 dh_installman make[1]: Leaving directory '/<>' dh_python3 -a -O--buildsystem=cmake dh_installsystemduser -a -O--buildsystem=cmake dh_perl -a -O--buildsystem=cmake dh_link -a -O--buildsystem=cmake dh_strip_nondeterminism -a -O--buildsystem=cmake dh_compress -a -O--buildsystem=cmake dh_fixperms -a -O--buildsystem=cmake dh_missing -a -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/python3-gemmi/usr/lib/python3/dist-packages/gemmi.cpython-312-aarch64-linux-gnu.so: .debug_info section not present dh_strip -a -O--buildsystem=cmake b68a2ae244f49d915b5d7246338f1184a954feb3 dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -a -O--buildsystem=cmake dh_gencontrol -a -O--buildsystem=cmake dpkg-gencontrol: warning: Provides field of package python3-gemmi: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -a -O--buildsystem=cmake dh_builddeb -a -O--buildsystem=cmake INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing python3-gemmi (in debian/python3-gemmi); do_strip: , oemstrip: pkgstriptranslations: processing gemmi (in debian/gemmi); do_strip: , oemstrip: pkgstriptranslations: processing gemmi-dev (in debian/gemmi-dev); do_strip: , oemstrip: pkgstriptranslations: processing gemmi-dbgsym (in debian/.debhelper/gemmi/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-gemmi/DEBIAN/control, package python3-gemmi, directory debian/python3-gemmi INFO: pkgstripfiles: waiting for lock (python3-gemmi) ... pkgstripfiles: processing control file: debian/gemmi/DEBIAN/control, package gemmi, directory debian/gemmi pkgstripfiles: Truncating usr/share/doc/gemmi/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package gemmi ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gemmi' in '../gemmi_0.6.4+ds-1build1_arm64.deb'. pkgstripfiles: processing control file: debian/gemmi-dev/DEBIAN/control, package gemmi-dev, directory debian/gemmi-dev pkgstripfiles: processing control file: debian/.debhelper/gemmi/dbgsym-root/DEBIAN/control, package gemmi-dbgsym, directory debian/.debhelper/gemmi/dbgsym-root dpkg-deb: building package 'gemmi-dbgsym' in 'debian/.debhelper/scratch-space/build-gemmi/gemmi-dbgsym_0.6.4+ds-1build1_arm64.deb'. pkgstripfiles: Truncating usr/share/doc/gemmi-dev/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package gemmi-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.6.4+ds-1build1_arm64.deb'. pkgstripfiles: Truncating usr/share/doc/python3-gemmi/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-gemmi ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.4+ds-1build1_arm64.deb'. Renaming gemmi-dbgsym_0.6.4+ds-1build1_arm64.deb to gemmi-dbgsym_0.6.4+ds-1build1_arm64.ddeb dpkg-genbuildinfo --build=any -O../gemmi_0.6.4+ds-1build1_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../gemmi_0.6.4+ds-1build1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-01-19T19:42:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gemmi_0.6.4+ds-1build1_arm64.changes: ------------------------------------- Format: 1.8 Date: Fri, 19 Jan 2024 19:22:28 +0000 Source: gemmi Binary: gemmi gemmi-dev python3-gemmi Built-For-Profiles: noudeb Architecture: arm64 Version: 0.6.4+ds-1build1 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: gemmi - library for structural biology - executable gemmi-dev - library for structural biology python3-gemmi - library for structural biology - Python module Changes: gemmi (0.6.4+ds-1build1) noble; urgency=medium . * No-change rebuild with Python 3.12 as default Checksums-Sha1: f678903da99af1df1bb0534aed6270402fc5cde6 17039846 gemmi-dbgsym_0.6.4+ds-1build1_arm64.ddeb 749a0838d80a3fed4c46085b1dcb669f3c14988c 1176332 gemmi-dev_0.6.4+ds-1build1_arm64.deb 756af08994b0bdd05df9f99534fd051925a1b0d2 8622 gemmi_0.6.4+ds-1build1_arm64.buildinfo 39590e294f8e11190a9d33367c6ce065828b0694 1021084 gemmi_0.6.4+ds-1build1_arm64.deb 8da09953a770a7586c9fd07974e969fa4032ec0b 2137718 python3-gemmi_0.6.4+ds-1build1_arm64.deb Checksums-Sha256: 788549e669af1cf8703f15b00f58d9c11d36be553fbafb03c40a2e0f265e13d1 17039846 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/<>/gemmi_0.6.4+ds-1build1_arm64.changes.new could not be renamed to /<>/gemmi_0.6.4+ds-1build1_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: gemmi Binary: gemmi gemmi-dbgsym gemmi-dev python3-gemmi Architecture: arm64 Version: 0.6.4+ds-1build1 Checksums-Md5: 00d3699ff51f8e8f44e3ea70350fbfb9 17039846 gemmi-dbgsym_0.6.4+ds-1build1_arm64.ddeb 07e39c623ac0cd7e9687383f66b5f14e 1176332 gemmi-dev_0.6.4+ds-1build1_arm64.deb e13b161c519de75733635d11a5c7431c 1021084 gemmi_0.6.4+ds-1build1_arm64.deb 358ff9ccb18633696687b47e3ca1fc78 2137718 python3-gemmi_0.6.4+ds-1build1_arm64.deb Checksums-Sha1: f678903da99af1df1bb0534aed6270402fc5cde6 17039846 gemmi-dbgsym_0.6.4+ds-1build1_arm64.ddeb 749a0838d80a3fed4c46085b1dcb669f3c14988c 1176332 gemmi-dev_0.6.4+ds-1build1_arm64.deb 39590e294f8e11190a9d33367c6ce065828b0694 1021084 gemmi_0.6.4+ds-1build1_arm64.deb 8da09953a770a7586c9fd07974e969fa4032ec0b 2137718 python3-gemmi_0.6.4+ds-1build1_arm64.deb Checksums-Sha256: 788549e669af1cf8703f15b00f58d9c11d36be553fbafb03c40a2e0f265e13d1 17039846 gemmi-dbgsym_0.6.4+ds-1build1_arm64.ddeb bcbdd320b8ebd2968932e53c179c809b3763a816b35ac076d4427284c262fc84 1176332 gemmi-dev_0.6.4+ds-1build1_arm64.deb ddcbf0e896f6269efeb1572517347b7642352d8d3096204479e833ef9acd14dc 1021084 gemmi_0.6.4+ds-1build1_arm64.deb 80c180d67d25d252b3b3a9a6c4446c41c524bd8c03a6ff6ce1e8b6e4f7aced4f 2137718 python3-gemmi_0.6.4+ds-1build1_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Fri, 19 Jan 2024 19:42:25 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13ubuntu6), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), binutils (= 2.41.90.20240115-1ubuntu1), binutils-aarch64-linux-gnu (= 2.41.90.20240115-1ubuntu1), binutils-common (= 2.41.90.20240115-1ubuntu1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), cmake (= 3.28.1-1), cmake-data (= 3.28.1-1), coreutils (= 9.4-2ubuntu2), cpp (= 4:13.2.0-2ubuntu1), cpp-13 (= 13.2.0-10ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.83), debhelper (= 13.11.9ubuntu1), debianutils (= 5.16), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 6.20231223), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), doctest-dev (= 2.4.11-1), dpkg (= 1.22.2ubuntu2), dpkg-dev (= 1.22.2ubuntu2), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-2ubuntu1), g++-13 (= 13.2.0-10ubuntu1), gcc (= 4:13.2.0-2ubuntu1), gcc-13 (= 13.2.0-10ubuntu1), gcc-13-base (= 13.2.0-10ubuntu1), gettext (= 0.21-14), gettext-base (= 0.21-14), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), help2man (= 1.49.3), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-4ubuntu1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.7.2-1ubuntu2), libasan8 (= 13.2.0-10ubuntu1), libatomic1 (= 13.2.0-10ubuntu1), libattr1 (= 1:2.5.1-5), libaudit-common (= 1:3.1.2-1), libaudit1 (= 1:3.1.2-1), libbinutils (= 2.41.90.20240115-1ubuntu1), libblas3 (= 3.11.0-2build1), libblkid1 (= 2.39.2-6ubuntu1), libbrotli1 (= 1.1.0-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-3ubuntu1), libc-dev-bin (= 2.38-3ubuntu1), libc6 (= 2.38-3ubuntu1), libc6-dev (= 2.38-3ubuntu1), libcap-ng0 (= 0.8.4-1), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-10ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.41.90.20240115-1ubuntu1), libctf0 (= 2.41.90.20240115-1ubuntu1), libcurl4 (= 8.5.0-2ubuntu1), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.11.9ubuntu1), libdpkg-perl (= 1.22.2ubuntu2), libdw1 (= 0.190-1), libelf1 (= 0.190-1), libexpat1 (= 2.5.0-2), libexpat1-dev (= 2.5.0-2), libffi8 (= 3.4.4-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-10ubuntu1), libgcc-s1 (= 13.2.0-10ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 13.2.0-10ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.1-4ubuntu7), libgomp1 (= 13.2.0-10ubuntu1), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.41.90.20240115-1ubuntu1), libgssapi-krb5-2 (= 1.20.1-5build1), libhogweed6 (= 3.9.1-2), libhwasan0 (= 13.2.0-10ubuntu1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.4-1build1), libisl23 (= 0.26-3), libitm1 (= 13.2.0-10ubuntu1), libjansson4 (= 2.14-2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 7.2.6-3), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjsoncpp25 (= 1.9.5-6), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), liblapack3 (= 3.11.0-2build1), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu2), liblocale-gettext-perl (= 1.07-6build1), liblsan0 (= 13.2.0-10ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.5-0.3), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-2), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20240113-1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.58.0-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libp11-kit0 (= 0.25.3-2ubuntu2), libpam-modules (= 1.5.2-9.1ubuntu2), libpam-modules-bin (= 1.5.2-9.1ubuntu2), libpam-runtime (= 1.5.2-9.1ubuntu2), libpam0g (= 1.5.2-9.1ubuntu2), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1), libproc2-0 (= 2:4.0.4-2ubuntu1), libpsl5 (= 0.21.2-1build1), libpython3-dev (= 3.12.1-0ubuntu1), libpython3-stdlib (= 3.12.1-0ubuntu1), libpython3.11-minimal (= 3.11.7-2), libpython3.11-stdlib (= 3.11.7-2), libpython3.12 (= 3.12.1-2), libpython3.12-dev (= 3.12.1-2), libpython3.12-minimal (= 3.12.1-2), libpython3.12-stdlib (= 3.12.1-2), libreadline8 (= 8.2-3), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.4-2ubuntu1), libselinux1 (= 3.5-1build2), libsframe1 (= 2.41.90.20240115-1ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libsqlite3-0 (= 3.44.2-1), libssh-4 (= 0.10.6-2), libssl3 (= 3.0.10-1ubuntu3), libstb-dev (= 0.0~git20230129.5736b15+ds-1), libstb0 (= 0.0~git20230129.5736b15+ds-1), libstdc++-13-dev (= 13.2.0-10ubuntu1), libstdc++6 (= 13.2.0-10ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.2-3ubuntu1), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1), libtirpc-common (= 1.3.4+ds-1build1), libtirpc-dev (= 1.3.4+ds-1build1), libtirpc3 (= 1.3.4+ds-1build1), libtool (= 2.4.7-7), libtsan2 (= 13.2.0-10ubuntu1), libubsan1 (= 13.2.0-10ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.2-3ubuntu1), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libuv1 (= 1.46.0-3), libxml2 (= 2.9.14+dfsg-1.3build3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.0-14.14), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 45), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20231126-1), media-types (= 10.1.0), ncurses-base (= 6.4+20240113-1), ncurses-bin (= 6.4+20240113-1), netbase (= 6.4), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-2ubuntu1), pybind11-dev (= 2.11.1-2), python3 (= 3.12.1-0ubuntu1), python3-dev (= 3.12.1-0ubuntu1), python3-distutils (= 3.11.5-1), python3-iniconfig (= 1.1.1-2), python3-lib2to3 (= 3.11.5-1), python3-minimal (= 3.12.1-0ubuntu1), python3-numpy (= 1:1.24.2-2), python3-packaging (= 23.2-1), python3-pkg-resources (= 68.1.2-2), python3-pluggy (= 1.3.0-1), python3-pybind11 (= 2.11.1-2), python3-pytest (= 7.4.4-1), python3-setuptools (= 68.1.2-2), python3.11 (= 3.11.7-2), python3.11-minimal (= 3.11.7-2), python3.12 (= 3.12.1-2), python3.12-dev (= 3.12.1-2), python3.12-minimal (= 3.12.1-2), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-3ubuntu1), tao-pegtl-dev (= 3.2.7-1), tar (= 1.35+dfsg-3), tzdata (= 2023d-1ubuntu2), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1705692148" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gemmi-dev_0.6.4+ds-1build1_arm64.deb ------------------------------------ new Debian package, version 2.0. size 1176332 bytes: control archive=3542 bytes. 820 bytes, 19 lines control 7165 bytes, 110 lines md5sums Package: gemmi-dev Source: gemmi Version: 0.6.4+ds-1build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 5937 Section: libdevel Priority: optional Homepage: https://project-gemmi.github.io Description: library for structural biology Library for macromolecular crystallography and structural bioinformatics. For working with coordinate files (mmCIF, PDB, mmJSON), refinement restraints (monomer library), electron density maps (CCP4), and crystallographic reflection data (MTZ, SF-mmCIF). It understands crystallographic symmetries, it knows how to switch between the real and reciprocal space and it can do a few other things. . This package contains header-only C++ library. drwxr-xr-x root/root 0 2024-01-19 19:22 ./ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/include/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/include/gemmi/ -rw-r--r-- root/root 844 2023-12-13 10:39 ./usr/include/gemmi/addends.hpp -rw-r--r-- root/root 11686 2023-12-13 10:39 ./usr/include/gemmi/align.hpp -rw-r--r-- root/root 4460 2023-12-13 10:39 ./usr/include/gemmi/assembly.hpp -rw-r--r-- root/root 7455 2023-12-13 10:39 ./usr/include/gemmi/asudata.hpp -rw-r--r-- root/root 11452 2023-12-13 10:39 ./usr/include/gemmi/asumask.hpp -rw-r--r-- root/root 1023 2023-12-13 10:39 ./usr/include/gemmi/atof.hpp -rw-r--r-- root/root 3810 2023-12-13 10:39 ./usr/include/gemmi/atox.hpp -rw-r--r-- root/root 3983 2023-12-13 10:39 ./usr/include/gemmi/bessel.hpp -rw-r--r-- root/root 7728 2023-12-13 10:39 ./usr/include/gemmi/binner.hpp -rw-r--r-- root/root 4864 2023-12-13 10:39 ./usr/include/gemmi/blob.hpp 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./usr/include/gemmi/grid.hpp -rw-r--r-- root/root 5164 2023-12-13 10:39 ./usr/include/gemmi/gz.hpp -rw-r--r-- root/root 4512 2023-12-13 10:39 ./usr/include/gemmi/input.hpp -rw-r--r-- root/root 1864 2023-12-13 10:39 ./usr/include/gemmi/interop.hpp -rw-r--r-- root/root 23738 2023-12-13 10:39 ./usr/include/gemmi/it92.hpp -rw-r--r-- root/root 10089 2023-12-13 10:39 ./usr/include/gemmi/iterator.hpp -rw-r--r-- root/root 4820 2023-12-13 10:39 ./usr/include/gemmi/json.hpp -rw-r--r-- root/root 9023 2023-12-13 10:39 ./usr/include/gemmi/levmar.hpp -rw-r--r-- root/root 6763 2023-12-13 10:39 ./usr/include/gemmi/linkhunt.hpp -rw-r--r-- root/root 15168 2023-12-13 10:39 ./usr/include/gemmi/math.hpp -rw-r--r-- root/root 16861 2023-12-13 10:39 ./usr/include/gemmi/merge.hpp -rw-r--r-- root/root 13775 2023-12-13 10:39 ./usr/include/gemmi/metadata.hpp -rw-r--r-- root/root 991 2023-12-13 10:39 ./usr/include/gemmi/mmcif.hpp -rw-r--r-- root/root 1200 2023-12-13 10:39 ./usr/include/gemmi/mmcif_impl.hpp 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./usr/include/gemmi/seqalign.hpp -rw-r--r-- root/root 5125 2023-12-13 10:39 ./usr/include/gemmi/seqid.hpp -rw-r--r-- root/root 2045 2023-12-13 10:39 ./usr/include/gemmi/seqtools.hpp -rw-r--r-- root/root 5631 2023-12-13 10:39 ./usr/include/gemmi/sfcalc.hpp -rw-r--r-- root/root 4034 2023-12-13 10:39 ./usr/include/gemmi/small.hpp -rw-r--r-- root/root 6800 2023-12-13 10:39 ./usr/include/gemmi/smcif.hpp -rw-r--r-- root/root 18223 2023-12-13 10:39 ./usr/include/gemmi/solmask.hpp -rw-r--r-- root/root 4668 2023-12-13 10:39 ./usr/include/gemmi/span.hpp -rw-r--r-- root/root 2368 2023-12-13 10:39 ./usr/include/gemmi/sprintf.hpp -rw-r--r-- root/root 2761 2023-12-13 10:39 ./usr/include/gemmi/stats.hpp -rw-r--r-- root/root 93860 2023-12-13 10:39 ./usr/include/gemmi/symmetry.hpp drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/include/gemmi/third_party/ -rw-r--r-- root/root 115334 2023-12-13 10:39 ./usr/include/gemmi/third_party/fast_float.h -rw-r--r-- root/root 107015 2023-12-13 10:39 ./usr/include/gemmi/third_party/pocketfft_hdronly.h -rw-r--r-- root/root 95912 2023-12-13 10:39 ./usr/include/gemmi/third_party/sajson.h -rw-r--r-- root/root 19231 2023-12-13 10:39 ./usr/include/gemmi/third_party/tinydir.h -rw-r--r-- root/root 3373 2023-12-13 10:39 ./usr/include/gemmi/to_chemcomp.hpp -rw-r--r-- root/root 7774 2023-12-13 10:39 ./usr/include/gemmi/to_cif.hpp -rw-r--r-- root/root 8862 2023-12-13 10:39 ./usr/include/gemmi/to_json.hpp -rw-r--r-- root/root 2361 2023-12-13 10:39 ./usr/include/gemmi/to_mmcif.hpp -rw-r--r-- root/root 2173 2023-12-13 10:39 ./usr/include/gemmi/to_pdb.hpp -rw-r--r-- root/root 11062 2023-12-13 10:39 ./usr/include/gemmi/topo.hpp -rw-r--r-- root/root 10321 2023-12-13 10:39 ./usr/include/gemmi/twin.hpp -rw-r--r-- root/root 21676 2023-12-13 10:39 ./usr/include/gemmi/unitcell.hpp -rw-r--r-- root/root 2433 2023-12-13 10:39 ./usr/include/gemmi/utf.hpp -rw-r--r-- root/root 9845 2023-12-13 10:39 ./usr/include/gemmi/util.hpp -rw-r--r-- root/root 152 2023-12-13 10:39 ./usr/include/gemmi/version.hpp -rw-r--r-- root/root 14985 2023-12-13 10:39 ./usr/include/gemmi/xds_ascii.hpp drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/aarch64-linux-gnu/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/aarch64-linux-gnu/cmake/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/aarch64-linux-gnu/cmake/gemmi/ -rw-r--r-- root/root 1861 2024-01-19 19:22 ./usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-config-version.cmake -rw-r--r-- root/root 1527 2024-01-19 19:22 ./usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-config.cmake -rw-r--r-- root/root 1259 2024-01-19 19:22 ./usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-targets-none.cmake -rw-r--r-- root/root 4845 2024-01-19 19:22 ./usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-targets.cmake -rw-r--r-- root/root 4439578 2024-01-19 19:22 ./usr/lib/aarch64-linux-gnu/libgemmi_cpp.a drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/gemmi-dev/ -rw-r--r-- root/root 802 2024-01-19 19:22 ./usr/share/doc/gemmi-dev/changelog.Debian.gz -rw-r--r-- root/root 7099 2023-12-19 07:33 ./usr/share/doc/gemmi-dev/copyright gemmi_0.6.4+ds-1build1_arm64.deb -------------------------------- new Debian package, version 2.0. size 1021084 bytes: control archive=848 bytes. 900 bytes, 19 lines control 250 bytes, 4 lines md5sums Package: gemmi Version: 0.6.4+ds-1build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 2267 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6) Section: science Priority: optional Homepage: https://project-gemmi.github.io Description: library for structural biology - executable Library for macromolecular crystallography and structural bioinformatics. For working with coordinate files (mmCIF, PDB, mmJSON), refinement restraints (monomer library), electron density maps (CCP4), and crystallographic reflection data (MTZ, SF-mmCIF). It understands crystallographic symmetries, it knows how to switch between the real and reciprocal space and it can do a few other things. . This package contains main gemmi executable. drwxr-xr-x root/root 0 2024-01-19 19:22 ./ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/bin/ -rwxr-xr-x root/root 2301200 2024-01-19 19:22 ./usr/bin/gemmi drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/gemmi/ -rw-r--r-- root/root 799 2024-01-19 19:22 ./usr/share/doc/gemmi/changelog.Debian.gz -rw-r--r-- root/root 7099 2023-12-19 07:33 ./usr/share/doc/gemmi/copyright drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/man/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/man/man1/ -rw-r--r-- root/root 885 2024-01-19 19:22 ./usr/share/man/man1/gemmi.1.gz python3-gemmi_0.6.4+ds-1build1_arm64.deb ---------------------------------------- new Debian package, version 2.0. size 2137718 bytes: control archive=877 bytes. 959 bytes, 20 lines control 257 bytes, 3 lines md5sums Package: python3-gemmi Source: gemmi Version: 0.6.4+ds-1build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 6984 Depends: python3 (<< 3.13), python3 (>= 3.12~), libc6 (>= 2.38), libgcc-s1 (>= 4.2), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6) Section: python Priority: optional Homepage: https://project-gemmi.github.io Description: library for structural biology - Python module Library for macromolecular crystallography and structural bioinformatics. For working with coordinate files (mmCIF, PDB, mmJSON), refinement restraints (monomer library), electron density maps (CCP4), and crystallographic reflection data (MTZ, SF-mmCIF). It understands crystallographic symmetries, it knows how to switch between the real and reciprocal space and it can do a few other things. . This package contains the Python module. drwxr-xr-x root/root 0 2024-01-19 19:22 ./ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 7132968 2024-01-19 19:22 ./usr/lib/python3/dist-packages/gemmi.cpython-312-aarch64-linux-gnu.so drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-19 19:22 ./usr/share/doc/python3-gemmi/ -rw-r--r-- root/root 804 2024-01-19 19:22 ./usr/share/doc/python3-gemmi/changelog.Debian.gz -rw-r--r-- root/root 7099 2023-12-19 07:33 ./usr/share/doc/python3-gemmi/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 1425668 Build-Time: 930 Distribution: noble-proposed Host Architecture: arm64 Install-Time: 58 Job: gemmi_0.6.4+ds-1build1.dsc Machine Architecture: arm64 Package: gemmi Package-Time: 990 Source-Version: 0.6.4+ds-1build1 Space: 1425668 Status: successful Version: 0.6.4+ds-1build1 -------------------------------------------------------------------------------- Finished at 2024-01-19T19:42:26Z Build needed 00:16:30, 1425668k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27660667 Scanning for processes to kill in build PACKAGEBUILD-27660667