https://launchpad.net/ubuntu/+source/gemmi/0.5.1+ds-1build1/+build/23053203 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-017 4.15.0-166-generic #174-Ubuntu SMP Wed Dec 8 19:07:44 UTC 2021 x86_64 Buildd toolchain package versions: launchpad-buildd_206~519~ubuntu18.04.1 python3-lpbuildd_206~519~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 15 Jan 06:00:10 ntpdate[1778]: adjust time server 10.131.248.1 offset -0.001283 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-23053203 --image-type chroot /home/buildd/filecache-default/b0c128df17a460089eca69348f06144377489985 Creating target for build PACKAGEBUILD-23053203 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-23053203 Starting target for build PACKAGEBUILD-23053203 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-23053203 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-23053203 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-23053203 Updating target for build PACKAGEBUILD-23053203 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 Packages [1412 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe amd64 Packages [13.4 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5592 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 Packages [167 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [60.4 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 Packages [656 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [241 kB] Fetched 22.6 MB in 2s (9910 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libssl1.1 Use 'sudo apt autoremove' to remove it. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: libsemanage2 libsepol2 libssl3 The following packages will be upgraded: apt base-files bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils bzip2 ca-certificates cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libbz2-1.0 libcap-ng0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdpkg-perl libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mount ncurses-base ncurses-bin openssl passwd pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv systemd-timesyncd tzdata usrmerge util-linux 112 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 84.5 MB of archives. After this operation, 354 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main amd64 debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main amd64 libpam0g amd64 1.4.0-10ubuntu2 [61.5 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main amd64 libcrypt-dev amd64 1:4.4.27-1 [112 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main amd64 libcrypt1 amd64 1:4.4.27-1 [82.0 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main amd64 base-files amd64 12ubuntu2 [63.3 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main amd64 debianutils amd64 5.5-1ubuntu1 [107 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 bash amd64 5.1-6ubuntu1 [769 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdutils amd64 1:2.37.2-4ubuntu1 [80.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libgpg-error0 amd64 1.43-2 [69.7 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main amd64 libgcrypt20 amd64 1.9.4-3ubuntu2 [515 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main amd64 bzip2 amd64 1.0.8-5 [34.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main amd64 libbz2-1.0 amd64 1.0.8-5 [34.5 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcc1-0 amd64 11.2.0-14ubuntu1 [53.6 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libctf0 amd64 2.37.50.20220106-2ubuntu1 [103 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libctf-nobfd0 amd64 2.37.50.20220106-2ubuntu1 [106 kB] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.37.50.20220106-2ubuntu1 [2329 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libbinutils amd64 2.37.50.20220106-2ubuntu1 [655 kB] Get:18 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 binutils-common amd64 2.37.50.20220106-2ubuntu1 [220 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 binutils amd64 2.37.50.20220106-2ubuntu1 [3200 B] Get:20 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 gcc-11-base amd64 11.2.0-14ubuntu1 [21.3 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libgcc-s1 amd64 11.2.0-14ubuntu1 [45.5 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libgomp1 amd64 11.2.0-14ubuntu1 [117 kB] Get:23 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libitm1 amd64 11.2.0-14ubuntu1 [30.0 kB] Get:24 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libatomic1 amd64 11.2.0-14ubuntu1 [9998 B] Get:25 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libasan6 amd64 11.2.0-14ubuntu1 [2284 kB] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 liblsan0 amd64 11.2.0-14ubuntu1 [976 kB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libtsan0 amd64 11.2.0-14ubuntu1 [2260 kB] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libubsan1 amd64 11.2.0-14ubuntu1 [921 kB] Get:29 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libquadmath0 amd64 11.2.0-14ubuntu1 [154 kB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 g++-11 amd64 11.2.0-14ubuntu1 [11.4 MB] Get:31 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libstdc++-11-dev amd64 11.2.0-14ubuntu1 [2103 kB] Get:32 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libgcc-11-dev amd64 11.2.0-14ubuntu1 [2532 kB] Get:33 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 gcc-11 amd64 11.2.0-14ubuntu1 [20.1 MB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 cpp-11 amd64 11.2.0-14ubuntu1 [9961 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libstdc++6 amd64 11.2.0-14ubuntu1 [655 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main amd64 libisl23 amd64 0.24-2 [728 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main amd64 libmpc3 amd64 1.2.1-1 [46.9 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main amd64 libzstd1 amd64 1.4.8+dfsg-3 [324 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main amd64 libssl3 amd64 3.0.1-0ubuntu1 [1898 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main amd64 libblkid1 amd64 2.37.2-4ubuntu1 [103 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main amd64 libuuid1 amd64 2.37.2-4ubuntu1 [23.8 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main amd64 libcryptsetup12 amd64 2:2.4.2-1ubuntu4 [208 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main amd64 libidn2-0 amd64 2.3.2-2 [66.5 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main amd64 libp11-kit0 amd64 0.24.0-6 [252 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main amd64 libtasn1-6 amd64 4.18.0-4 [42.9 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main amd64 libgnutls30 amd64 3.7.2-5ubuntu1 [956 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd-sysv amd64 249.5-2ubuntu4 [10.5 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd-timesyncd amd64 249.5-2ubuntu4 [30.9 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main amd64 libapparmor1 amd64 3.0.3-0ubuntu5 [38.0 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main amd64 libip4tc2 amd64 1.8.7-1ubuntu4 [19.8 kB] Get:51 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libkmod2 amd64 29-1ubuntu1 [48.0 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main amd64 libpcre2-8-0 amd64 10.39-3 [220 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libselinux1 amd64 3.3-1build1 [74.5 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main amd64 libmount1 amd64 2.37.2-4ubuntu1 [122 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main amd64 libseccomp2 amd64 2.5.2-2ubuntu2 [48.3 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main amd64 login amd64 1:4.8.1-2ubuntu1 [188 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main amd64 util-linux amd64 2.37.2-4ubuntu1 [1063 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main amd64 mount amd64 2.37.2-4ubuntu1 [114 kB] Get:59 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 systemd amd64 249.5-2ubuntu4 [4544 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsystemd0 amd64 249.5-2ubuntu4 [318 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libudev1 amd64 249.5-2ubuntu4 [78.0 kB] Get:62 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libxxhash0 amd64 0.8.1-1 [27.3 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main amd64 libapt-pkg6.0 amd64 2.3.14 [905 kB] Get:64 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 dpkg amd64 1.21.1ubuntu1 [1254 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-3 [91.8 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main amd64 grep amd64 3.7-1 [156 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main amd64 libncurses6 amd64 6.3-1 [111 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main amd64 libncursesw6 amd64 6.3-1 [147 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main amd64 libtinfo6 amd64 6.3-1 [104 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-bin amd64 6.3-1 [184 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main amd64 sed amd64 4.8-1ubuntu1 [188 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main amd64 init-system-helpers all 1.61 [39.3 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main amd64 ncurses-base all 6.3-1 [19.9 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgv amd64 2.2.27-3ubuntu1 [137 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main amd64 apt amd64 2.3.14 [1387 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main amd64 libsepol2 amd64 3.3-1 [281 kB] Get:77 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsemanage-common all 3.3-1build1 [10.0 kB] Get:78 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsemanage2 amd64 3.3-1build1 [92.4 kB] Get:79 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http://ftpmaster.internal/ubuntu jammy/main amd64 ca-certificates all 20211016 [148 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main amd64 readline-common all 8.1.2-1 [53.5 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/main amd64 libreadline8 amd64 8.1.2-1 [153 kB] Get:102 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libsqlite3-0 amd64 3.37.2-1 [642 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main amd64 tzdata all 2021e-1ubuntu1 [343 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main amd64 libgdbm6 amd64 1.22-1 [35.2 kB] Get:105 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 dpkg-dev all 1.21.1ubuntu1 [922 kB] Get:106 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libdpkg-perl all 1.21.1ubuntu1 [236 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/main amd64 make amd64 4.3-4ubuntu2 [179 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main amd64 lto-disabled-list all 18 [12.2 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg amd64 2.2.27-3ubuntu1 [517 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/main amd64 gpgconf amd64 2.2.27-3ubuntu1 [94.4 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/main amd64 gpg-agent amd64 2.2.27-3ubuntu1 [209 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main amd64 libgdbm-compat4 amd64 1.22-1 [6450 B] Get:113 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 linux-libc-dev amd64 5.15.0-17.17 [1255 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/main amd64 lockfile-progs amd64 0.1.19 [10.0 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/main amd64 pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.5 MB in 1s (109 MB/s) (Reading database ... 13258 files and directories currently installed.) Preparing to unpack .../debconf_1.5.79_all.deb ... Unpacking debconf (1.5.79) over (1.5.77) ... Setting up debconf (1.5.79) ... (Reading database ... 13257 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-10ubuntu2_amd64.deb ... Unpacking libpam0g:amd64 (1.4.0-10ubuntu2) over (1.3.1-5ubuntu11) ... Setting up libpam0g:amd64 (1.4.0-10ubuntu2) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 13257 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.27-1_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Preparing to unpack .../libcrypt1_1%3a4.4.27-1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Setting up libcrypt1:amd64 (1:4.4.27-1) ... (Reading database ... 13257 files and directories currently installed.) Preparing to unpack .../base-files_12ubuntu2_amd64.deb ... 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Setting up linux-libc-dev:amd64 (5.15.0-17.17) ... Setting up libctf-nobfd0:amd64 (2.37.50.20220106-2ubuntu1) ... Setting up libgomp1:amd64 (11.2.0-14ubuntu1) ... Setting up bzip2 (1.0.8-5) ... Setting up libasan6:amd64 (11.2.0-14ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jan 15 06:00:31 UTC 2022. Universal Time is now: Sat Jan 15 06:00:31 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:amd64 (6.3-1) ... Setting up libquadmath0:amd64 (11.2.0-14ubuntu1) ... Setting up libmpc3:amd64 (1.2.1-1) ... Setting up systemd-timesyncd (249.5-2ubuntu4) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:amd64 (11.2.0-14ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:amd64 (1.46.5-2ubuntu1) ... Setting up libncursesw6:amd64 (6.3-1) ... Setting up libdpkg-perl (1.21.1ubuntu1) ... Setting up logsave (1.46.5-2ubuntu1) ... 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Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up libgdbm-compat4:amd64 (1.22-1) ... Setting up libgcc-11-dev:amd64 (11.2.0-14ubuntu1) ... Setting up gpgconf (2.2.27-3ubuntu1) ... Setting up gpg (2.2.27-3ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.37.50.20220106-2ubuntu1) ... Setting up gpg-agent (2.2.27-3ubuntu1) ... Setting up binutils (2.37.50.20220106-2ubuntu1) ... Setting up dpkg-dev (1.21.1ubuntu1) ... Setting up libstdc++-11-dev:amd64 (11.2.0-14ubuntu1) ... Setting up gcc-11 (11.2.0-14ubuntu1) ... Setting up g++-11 (11.2.0-14ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23053203 amd64 jammy-proposed -c chroot:build-PACKAGEBUILD-23053203 --arch=amd64 --dist=jammy-proposed --nolog -A gemmi_0.5.1+ds-1build1.dsc Initiating build PACKAGEBUILD-23053203 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-166-generic #174-Ubuntu SMP Wed Dec 8 19:07:44 UTC 2021 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lcy02-amd64-017.buildd +==============================================================================+ | gemmi 0.5.1+ds-1build1 (amd64) Sat, 15 Jan 2022 06:00:34 +0000 | +==============================================================================+ Package: gemmi Version: 0.5.1+ds-1build1 Source Version: 0.5.1+ds-1build1 Distribution: jammy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23053203/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gemmi_0.5.1+ds-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/gemmi-BAGwRH/gemmi-0.5.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/gemmi-BAGwRH' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-7ShzR1/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-7ShzR1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7ShzR1/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-7ShzR1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7ShzR1/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-7ShzR1/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-7ShzR1/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13460 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), dh-python, help2man, libstb-dev, python3-dev, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev Filtered Build-Depends: cmake, debhelper-compat (= 13), dh-python, help2man, libstb-dev, python3-dev, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-gemmi-dummy' in '/<>/resolver-7ShzR1/apt_archive/sbuild-build-depends-gemmi-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gemmi-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-7ShzR1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-7ShzR1/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-7ShzR1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-7ShzR1/apt_archive ./ Sources [567 B] Get:5 copy:/<>/resolver-7ShzR1/apt_archive ./ Packages [637 B] Fetched 2167 B in 0s (0 B/s) Reading package lists... Reading package lists... Install gemmi build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libssl1.1 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-elpa-helper dh-python dh-strip-nondeterminism dwz emacsen-common file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbsd0 libcurl4 libdebhelper-perl libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libicu67 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp25 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libmd0 libmpdec3 libnghttp2-14 libpipeline1 libpsl5 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libstb-dev libstb0 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db media-types po-debconf pybind11-dev python3 python3-attr python3-dev python3-distutils python3-importlib-metadata python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pybind11 python3-pyparsing python3-pytest python3-toml python3-zipp python3.10 python3.10-dev python3.10-minimal tao-pegtl-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build cmake-format dh-make flit python3-build python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl pybind11-doc python3-doc python3-tk python3-venv python-attr-doc python3-setuptools subversion python-pyparsing-doc python3.10-venv python3.10-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl libeigen3-dev python3-numpy python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-elpa-helper dh-python dh-strip-nondeterminism dwz emacsen-common file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbsd0 libcurl4 libdebhelper-perl libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libicu67 libjs-jquery libjs-sphinxdoc libjs-underscore libjsoncpp25 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libmd0 libmpdec3 libnghttp2-14 libpipeline1 libpsl5 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libstb-dev libstb0 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db media-types po-debconf pybind11-dev python3 python3-attr python3-dev python3-distutils python3-importlib-metadata python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pybind11 python3-pyparsing python3-pytest python3-toml python3-zipp python3.10 python3.10-dev python3.10-minimal sbuild-build-depends-gemmi-dummy tao-pegtl-dev zlib1g-dev 0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 42.7 MB of archives. After this operation, 162 MB of additional disk space will be used. Get:1 copy:/<>/resolver-7ShzR1/apt_archive ./ sbuild-build-depends-gemmi-dummy 0.invalid.0 [726 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main amd64 liblocale-gettext-perl amd64 1.07-4build2 [17.1 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libpython3.10-minimal amd64 3.10.1-5 [808 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main amd64 libexpat1 amd64 2.4.2-1 [90.1 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3.10-minimal amd64 3.10.1-5 [2096 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3-minimal amd64 3.10.1-0ubuntu1 [24.7 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main amd64 media-types all 4.0.0 [22.2 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main amd64 libmd0 amd64 1.0.4-1 [22.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main amd64 libbsd0 amd64 0.11.3-1ubuntu3 [44.7 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main amd64 libedit2 amd64 3.1-20210910-1 [96.5 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main amd64 libmpdec3 amd64 2.5.1-2build1 [86.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libpython3.10-stdlib amd64 3.10.1-5 [1824 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3.10 amd64 3.10.1-5 [480 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libpython3-stdlib amd64 3.10.1-0ubuntu1 [7320 B] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3 amd64 3.10.1-0ubuntu1 [22.8 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main amd64 libelf1 amd64 0.186-1 [51.4 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main amd64 libicu67 amd64 67.1-7ubuntu1 [10.1 MB] Get:18 http://ftpmaster.internal/ubuntu jammy/main amd64 libxml2 amd64 2.9.12+dfsg-5 [761 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 python3-pkg-resources all 59.6.0-1.1 [132 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main amd64 bsdextrautils amd64 2.37.2-4ubuntu1 [71.1 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main amd64 libmagic-mgc amd64 1:5.41-2 [257 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main amd64 libmagic1 amd64 1:5.41-2 [87.3 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main amd64 file amd64 1:5.41-2 [21.5 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main amd64 gettext-base amd64 0.21-4ubuntu3 [36.6 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main amd64 libuchardet0 amd64 0.0.7-1build1 [76.7 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main amd64 groff-base amd64 1.22.4-8 [952 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main amd64 libpipeline1 amd64 1.5.5-1 [23.5 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main amd64 libpsl5 amd64 0.21.0-1.2build1 [57.5 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main amd64 libuv1 amd64 1.42.0-1 [92.3 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main amd64 man-db amd64 2.9.4-4 [1179 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main amd64 libsigsegv2 amd64 2.13-1ubuntu2 [14.6 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main amd64 m4 amd64 1.4.18-5ubuntu1 [199 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main amd64 autoconf all 2.71-2 [338 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main amd64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main amd64 automake all 1:1.16.5-1.1 [558 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main amd64 autopoint all 0.21-4ubuntu3 [422 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main amd64 libarchive13 amd64 3.5.2-1 [366 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main amd64 libbrotli1 amd64 1.0.9-2build4 [315 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg2-3 [20.6 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main amd64 libsasl2-2 amd64 2.1.27+dfsg2-3 [53.8 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main amd64 libldap-2.5-0 amd64 2.5.6+dfsg-1~exp1ubuntu1 [186 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main amd64 libnghttp2-14 amd64 1.43.0-1build2 [76.2 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build3 [58.3 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main amd64 libssh-4 amd64 0.9.6-2 [184 kB] Get:45 http://ftpmaster.internal/ubuntu jammy-proposed/main amd64 libcurl4 amd64 7.81.0-1 [288 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main amd64 libjsoncpp25 amd64 1.9.5-2 [80.0 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main amd64 librhash0 amd64 1.4.2-1 [125 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-elpa-helper all 2.0.9ubuntu1 [7610 B] Get:49 http://ftpmaster.internal/ubuntu jammy/main amd64 emacsen-common all 3.0.4 [14.9 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main amd64 cmake-data all 3.22.1-1ubuntu1 [1912 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main amd64 cmake amd64 3.22.1-1ubuntu1 [5012 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main amd64 libdebhelper-perl all 13.5.2ubuntu1 [66.0 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main amd64 libtool all 2.4.6-15build1 [164 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-autoreconf all 20 [16.1 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:57 http://ftpmaster.internal/ubuntu jammy/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main amd64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:59 http://ftpmaster.internal/ubuntu jammy/main amd64 libdw1 amd64 0.186-1 [251 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main amd64 debugedit amd64 1:5.0-4 [47.1 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main amd64 dwz amd64 0.14-1build1 [104 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main amd64 gettext amd64 0.21-4ubuntu3 [824 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main amd64 debhelper all 13.5.2ubuntu1 [926 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main amd64 python3-lib2to3 all 3.9.9-3 [77.7 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main amd64 python3-distutils all 3.9.9-3 [144 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/universe amd64 dh-python all 5.20220101 [103 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/universe amd64 help2man amd64 1.48.5 [139 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main amd64 libexpat1-dev amd64 2.4.2-1 [147 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-8 [321 kB] Get:72 http://ftpmaster.internal/ubuntu 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python3-py all 1.10.0-1 [71.9 kB] Get:92 http://ftpmaster.internal/ubuntu jammy-proposed/universe amd64 python3-pybind11 all 2.9.0-1 [155 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/universe amd64 python3-pytest all 6.2.5-1ubuntu1 [214 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/universe amd64 tao-pegtl-dev all 2.8.3-3 [49.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.7 MB in 0s (118 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.5.2ubuntu1) ... Setting up libbrotli1:amd64 (1.0.9-2build4) ... Setting up libnghttp2-14:amd64 (1.43.0-1build2) ... Setting up libmagic1:amd64 (1:5.41-2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up file (1:5.41-2) ... Setting up pybind11-dev (2.9.0-1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg2-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:amd64 (1.42.0-1) ... Setting up libexpat1-dev:amd64 (2.4.2-1) ... Setting up emacsen-common (3.0.4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build3) ... Setting up dh-elpa-helper (2.0.9ubuntu1) ... Setting up libsigsegv2:amd64 (2.13-1ubuntu2) ... Setting up libstb0:amd64 (0.0~git20200713.b42009b+ds-1) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up libjsoncpp25:amd64 (1.9.5-2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg2-3) ... Setting up libssh-4:amd64 (0.9.6-2) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu7) ... Setting up libmd0:amd64 (1.0.4-1) ... Setting up libstb-dev:amd64 (0.0~git20200713.b42009b+ds-1) ... Setting up librhash0:amd64 (1.4.2-1) ... Setting up libuchardet0:amd64 (0.0.7-1build1) ... Setting up libmpdec3:amd64 (2.5.1-2build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up cmake-data (3.22.1-1ubuntu1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-8) ... Setting up libbsd0:amd64 (0.11.3-1ubuntu3) ... Setting up libelf1:amd64 (0.186-1) ... Setting up libxml2:amd64 (2.9.12+dfsg-5) ... Setting up liblocale-gettext-perl (1.07-4build2) ... Setting up tao-pegtl-dev (2.8.3-3) ... Setting up libjs-underscore (1.9.1~dfsg-4) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:amd64 (0.186-1) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libtool (2.4.6-15build1) ... Setting up libarchive13:amd64 (3.5.2-1) ... Setting up libedit2:amd64 (3.1-20210910-1) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libldap-2.5-0:amd64 (2.5.6+dfsg-1~exp1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.5) ... Setting up libpython3.10-stdlib:amd64 (3.10.1-5) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-8) ... Setting up debugedit (1:5.0-4) ... Setting up libcurl4:amd64 (7.81.0-1) ... Setting up libpython3-stdlib:amd64 (3.10.1-0ubuntu1) ... Setting up automake (1:1.16.5-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.10:amd64 (3.10.1-5) ... Setting up python3.10 (3.10.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.10.1-0ubuntu1) ... Setting up man-db (2.9.4-4) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up dh-autoreconf (20) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up libpython3.10-dev:amd64 (3.10.1-5) ... Setting up python3-toml (0.10.2-1) ... Setting up python3.10-dev (3.10.1-5) ... Setting up cmake (3.22.1-1ubuntu1) ... Setting up python3-lib2to3 (3.9.9-3) ... Setting up python3-pybind11 (2.9.0-1) ... Setting up python3-pkg-resources (59.6.0-1.1) ... Setting up python3-distutils (3.9.9-3) ... Setting up dh-python (5.20220101) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-1) ... Setting up python3-attr (20.3.0-1ubuntu1) ... Setting up libpython3-dev:amd64 (3.10.1-0ubuntu1) ... Setting up python3-py (1.10.0-1) ... Setting up debhelper (13.5.2ubuntu1) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-packaging (21.3-1) ... Setting up python3-dev (3.10.1-0ubuntu1) ... Setting up python3-importlib-metadata (4.6.4-1) ... Setting up python3-pluggy (0.13.0-7.1) ... Setting up python3-pytest (6.2.5-1ubuntu1) ... Setting up sbuild-build-depends-gemmi-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-166-generic amd64 (x86_64) Toolchain package versions: binutils_2.37.50.20220106-2ubuntu1 dpkg-dev_1.21.1ubuntu1 g++-11_11.2.0-14ubuntu1 gcc-11_11.2.0-14ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-14ubuntu1 libstdc++6_11.2.0-14ubuntu1 linux-libc-dev_5.15.0-17.17 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.14 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-6ubuntu1 binutils_2.37.50.20220106-2ubuntu1 binutils-common_2.37.50.20220106-2ubuntu1 binutils-x86-64-linux-gnu_2.37.50.20220106-2ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-5 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liblsan0_11.2.0-14ubuntu1 liblz4-1_1.9.3-2build1 liblzma5_5.2.5-2build1 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmd0_1.0.4-1 libmount1_2.37.2-4ubuntu1 libmpc3_1.2.1-1 libmpdec3_2.5.1-2build1 libmpfr6_4.1.0-3build2 libncurses6_6.3-1 libncursesw6_6.3-1 libnettle8_3.7.3-1build1 libnghttp2-14_1.43.0-1build2 libnpth0_1.6-3build1 libnsl-dev_1.3.0-2build1 libnsl2_1.3.0-2build1 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-10ubuntu2 libpam-modules-bin_1.4.0-10ubuntu2 libpam-runtime_1.4.0-10ubuntu2 libpam0g_1.4.0-10ubuntu2 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13build4 libperl5.32_5.32.1-3ubuntu3 libpipeline1_1.5.5-1 libpng16-16_1.6.37-3build4 libprocps8_2:3.3.17-5ubuntu3 libpsl5_0.21.0-1.2build1 libpython3-dev_3.10.1-0ubuntu1 libpython3-stdlib_3.10.1-0ubuntu1 libpython3.10_3.10.1-5 libpython3.10-dev_3.10.1-5 libpython3.10-minimal_3.10.1-5 libpython3.10-stdlib_3.10.1-5 libquadmath0_11.2.0-14ubuntu1 libreadline8_8.1.2-1 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2build3 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logsave_1.46.5-2ubuntu1 lsb-base_11.1.0ubuntu3 lto-disabled-list_18 m4_1.4.18-5ubuntu1 make_4.3-4ubuntu2 man-db_2.9.4-4 mawk_1.3.4.20200120-2build1 media-types_4.0.0 mount_2.37.2-4ubuntu1 ncurses-base_6.3-1 ncurses-bin_6.3-1 openssl_3.0.1-0ubuntu1 optipng_0.7.7-2 passwd_1:4.8.1-2ubuntu1 patch_2.7.6-7build1 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1build1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 pybind11-dev_2.9.0-1 python3_3.10.1-0ubuntu1 python3-attr_20.3.0-1ubuntu1 python3-dev_3.10.1-0ubuntu1 python3-distutils_3.9.9-3 python3-importlib-metadata_4.6.4-1 python3-iniconfig_1.1.1-1 python3-lib2to3_3.9.9-3 python3-minimal_3.10.1-0ubuntu1 python3-more-itertools_8.10.0-2 python3-packaging_21.3-1 python3-pkg-resources_59.6.0-1.1 python3-pluggy_0.13.0-7.1 python3-py_1.10.0-1 python3-pybind11_2.9.0-1 python3-pyparsing_2.4.7-1 python3-pytest_6.2.5-1ubuntu1 python3-toml_0.10.2-1 python3-zipp_1.0.0-3 python3.10_3.10.1-5 python3.10-dev_3.10.1-5 python3.10-minimal_3.10.1-5 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-0ubuntu5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gemmi-dummy_0.invalid.0 sed_4.8-1ubuntu1 sensible-utils_0.0.17 systemd_249.5-2ubuntu4 systemd-sysv_249.5-2ubuntu4 systemd-timesyncd_249.5-2ubuntu4 sysvinit-utils_2.96-7ubuntu2 tao-pegtl-dev_2.8.3-3 tar_1.34+dfsg-1build2 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Jan 13 19:16:32 2022 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./gemmi_0.5.1+ds-1build1.dsc dpkg-source: info: extracting gemmi in /<>/gemmi-0.5.1+ds dpkg-source: info: unpacking gemmi_0.5.1+ds.orig.tar.xz dpkg-source: info: unpacking gemmi_0.5.1+ds-1build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-tao-pegtl.patch dpkg-source: info: applying change_error_type_in_test.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-23053203 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23053203 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23053203 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.5.1+ds-1build1 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake --with python3 dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem=cmake --with python3 dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/gemmi-0.5.1+ds' dh_auto_configure -- -DUSE_PYTHON=1 -DINSTALL_EGG_INFO=OFF cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DUSE_PYTHON=1 -DINSTALL_EGG_INFO=OFF .. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Skipping Fortran bindings. Add -D USE_FORTRAN=1 to build them. -- Compiling with C++ standard: 17 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Benchmarks not configured. -- The python module will be built. -- Found PythonInterp: /usr/bin/python3.10 (found version "3.10.1") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.10.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.9.0") -- Found pybind11 2.9.0: /usr/include;/usr/include/python3.10 -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>/gemmi-0.5.1+ds' dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/gemmi-0.5.1+ds -B/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/depend make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/depend make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/depend make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds 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CMakeFiles/output.dir/build.make CMakeFiles/output.dir/build make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 0%] Building CXX object CMakeFiles/input.dir/src/input.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/input.dir/src/input.cpp.o -MF CMakeFiles/input.dir/src/input.cpp.o.d -o CMakeFiles/input.dir/src/input.cpp.o -c /<>/gemmi-0.5.1+ds/src/input.cpp [ 2%] Building CXX object CMakeFiles/options.dir/src/options.cpp.o [ 4%] Building CXX object CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/output.dir/src/output.cpp.o -MF CMakeFiles/output.dir/src/output.cpp.o.d -o CMakeFiles/output.dir/src/output.cpp.o -c /<>/gemmi-0.5.1+ds/src/output.cpp In file included from /<>/gemmi-0.5.1+ds/src/output.cpp:6: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. 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It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 14%] Building CXX object CMakeFiles/py.dir/python/ccp4.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/ccp4.cpp.o -MF CMakeFiles/py.dir/python/ccp4.cpp.o.d -o CMakeFiles/py.dir/python/ccp4.cpp.o -c /<>/gemmi-0.5.1+ds/python/ccp4.cpp [ 14%] Building CXX object CMakeFiles/py.dir/python/chemcomp.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/chemcomp.cpp.o -MF CMakeFiles/py.dir/python/chemcomp.cpp.o.d -o CMakeFiles/py.dir/python/chemcomp.cpp.o -c /<>/gemmi-0.5.1+ds/python/chemcomp.cpp make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 14%] Built target input [ 17%] Building CXX object CMakeFiles/py.dir/python/cif.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/cif.cpp.o -MF CMakeFiles/py.dir/python/cif.cpp.o.d -o CMakeFiles/py.dir/python/cif.cpp.o -c /<>/gemmi-0.5.1+ds/python/cif.cpp [ 19%] Building CXX object CMakeFiles/py.dir/python/custom.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/custom.cpp.o -MF CMakeFiles/py.dir/python/custom.cpp.o.d -o CMakeFiles/py.dir/python/custom.cpp.o -c /<>/gemmi-0.5.1+ds/python/custom.cpp [ 19%] Building CXX object CMakeFiles/py.dir/python/elem.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto 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/<>/gemmi-0.5.1+ds/python/meta.cpp [ 26%] Building CXX object CMakeFiles/py.dir/python/monlib.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/monlib.cpp.o -MF CMakeFiles/py.dir/python/monlib.cpp.o.d -o CMakeFiles/py.dir/python/monlib.cpp.o -c /<>/gemmi-0.5.1+ds/python/monlib.cpp [ 29%] Building CXX object CMakeFiles/py.dir/python/mtz.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -Wno-psabi -MD -MT CMakeFiles/py.dir/python/mtz.cpp.o -MF CMakeFiles/py.dir/python/mtz.cpp.o.d -o CMakeFiles/py.dir/python/mtz.cpp.o -c /<>/gemmi-0.5.1+ds/python/mtz.cpp [ 31%] Building CXX object CMakeFiles/py.dir/python/read.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/read.cpp.o -MF CMakeFiles/py.dir/python/read.cpp.o.d -o CMakeFiles/py.dir/python/read.cpp.o -c /<>/gemmi-0.5.1+ds/python/read.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/smcif.hpp:12, from /<>/gemmi-0.5.1+ds/python/read.cpp:7: 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-I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sf.cpp.o -MF CMakeFiles/py.dir/python/sf.cpp.o.d -o CMakeFiles/py.dir/python/sf.cpp.o -c /<>/gemmi-0.5.1+ds/python/sf.cpp [ 39%] Building CXX object CMakeFiles/py.dir/python/sym.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sym.cpp.o -MF CMakeFiles/py.dir/python/sym.cpp.o.d -o CMakeFiles/py.dir/python/sym.cpp.o -c /<>/gemmi-0.5.1+ds/python/sym.cpp [ 41%] Building CXX object CMakeFiles/py.dir/python/topo.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/topo.cpp.o -MF CMakeFiles/py.dir/python/topo.cpp.o.d -o CMakeFiles/py.dir/python/topo.cpp.o -c /<>/gemmi-0.5.1+ds/python/topo.cpp [ 43%] Building CXX object CMakeFiles/py.dir/python/unitcell.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/unitcell.cpp.o -MF CMakeFiles/py.dir/python/unitcell.cpp.o.d -o CMakeFiles/py.dir/python/unitcell.cpp.o -c /<>/gemmi-0.5.1+ds/python/unitcell.cpp [ 43%] Building CXX object CMakeFiles/py.dir/python/write.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/write.cpp.o -MF CMakeFiles/py.dir/python/write.cpp.o.d -o CMakeFiles/py.dir/python/write.cpp.o -c /<>/gemmi-0.5.1+ds/python/write.cpp In file included from /<>/gemmi-0.5.1+ds/python/write.cpp:4: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/depend make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/program.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/build make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 46%] Building CXX object CMakeFiles/program.dir/src/align.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/align.cpp.o -MF CMakeFiles/program.dir/src/align.cpp.o.d -o CMakeFiles/program.dir/src/align.cpp.o -c /<>/gemmi-0.5.1+ds/src/align.cpp [ 48%] Building CXX object CMakeFiles/program.dir/src/blobs.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/blobs.cpp.o -MF CMakeFiles/program.dir/src/blobs.cpp.o.d -o CMakeFiles/program.dir/src/blobs.cpp.o -c /<>/gemmi-0.5.1+ds/src/blobs.cpp [ 48%] Building CXX object CMakeFiles/program.dir/src/cif2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/cif2mtz.cpp.o -MF CMakeFiles/program.dir/src/cif2mtz.cpp.o.d -o CMakeFiles/program.dir/src/cif2mtz.cpp.o -c /<>/gemmi-0.5.1+ds/src/cif2mtz.cpp [ 51%] Building CXX object CMakeFiles/program.dir/src/cif2json.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/cif2json.cpp.o -MF CMakeFiles/program.dir/src/cif2json.cpp.o.d -o CMakeFiles/program.dir/src/cif2json.cpp.o -c /<>/gemmi-0.5.1+ds/src/cif2json.cpp [ 53%] Building CXX object CMakeFiles/program.dir/src/contact.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/contact.cpp.o -MF CMakeFiles/program.dir/src/contact.cpp.o.d -o CMakeFiles/program.dir/src/contact.cpp.o -c /<>/gemmi-0.5.1+ds/src/contact.cpp [ 56%] Linking CXX shared module gemmi.cpython-310-x86_64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/py.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -flto -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -shared -o gemmi.cpython-310-x86_64-linux-gnu.so CMakeFiles/py.dir/python/mol.cpp.o CMakeFiles/py.dir/python/gemmi.cpp.o CMakeFiles/py.dir/python/align.cpp.o CMakeFiles/py.dir/python/ccp4.cpp.o CMakeFiles/py.dir/python/chemcomp.cpp.o CMakeFiles/py.dir/python/cif.cpp.o CMakeFiles/py.dir/python/custom.cpp.o CMakeFiles/py.dir/python/elem.cpp.o CMakeFiles/py.dir/python/grid.cpp.o CMakeFiles/py.dir/python/hkl.cpp.o CMakeFiles/py.dir/python/meta.cpp.o CMakeFiles/py.dir/python/monlib.cpp.o CMakeFiles/py.dir/python/mtz.cpp.o CMakeFiles/py.dir/python/read.cpp.o CMakeFiles/py.dir/python/recgrid.cpp.o CMakeFiles/py.dir/python/scaling.cpp.o CMakeFiles/py.dir/python/search.cpp.o CMakeFiles/py.dir/python/sf.cpp.o CMakeFiles/py.dir/python/sym.cpp.o CMakeFiles/py.dir/python/topo.cpp.o CMakeFiles/py.dir/python/unitcell.cpp.o CMakeFiles/py.dir/python/write.cpp.o /usr/lib/x86_64-linux-gnu/libz.so [ 58%] Building CXX object CMakeFiles/program.dir/src/contents.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/contents.cpp.o -MF CMakeFiles/program.dir/src/contents.cpp.o.d -o CMakeFiles/program.dir/src/contents.cpp.o -c /<>/gemmi-0.5.1+ds/src/contents.cpp [ 58%] Building CXX object CMakeFiles/program.dir/src/convert.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/convert.cpp.o -MF CMakeFiles/program.dir/src/convert.cpp.o.d -o CMakeFiles/program.dir/src/convert.cpp.o -c /<>/gemmi-0.5.1+ds/src/convert.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /<>/gemmi-0.5.1+ds/src/convert.cpp:16: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 60%] Building CXX object CMakeFiles/program.dir/src/fprime.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/fprime.cpp.o -MF CMakeFiles/program.dir/src/fprime.cpp.o.d -o CMakeFiles/program.dir/src/fprime.cpp.o -c /<>/gemmi-0.5.1+ds/src/fprime.cpp [ 63%] Building CXX object CMakeFiles/program.dir/src/grep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/grep.cpp.o -MF CMakeFiles/program.dir/src/grep.cpp.o.d -o CMakeFiles/program.dir/src/grep.cpp.o -c /<>/gemmi-0.5.1+ds/src/grep.cpp [ 63%] Building CXX object CMakeFiles/program.dir/src/h.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/h.cpp.o -MF CMakeFiles/program.dir/src/h.cpp.o.d -o CMakeFiles/program.dir/src/h.cpp.o -c /<>/gemmi-0.5.1+ds/src/h.cpp [ 65%] Building CXX object CMakeFiles/program.dir/src/json2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/json2cif.cpp.o -MF CMakeFiles/program.dir/src/json2cif.cpp.o.d -o CMakeFiles/program.dir/src/json2cif.cpp.o -c /<>/gemmi-0.5.1+ds/src/json2cif.cpp [ 68%] Building CXX object CMakeFiles/program.dir/src/main.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/main.cpp.o -MF CMakeFiles/program.dir/src/main.cpp.o.d -o CMakeFiles/program.dir/src/main.cpp.o -c /<>/gemmi-0.5.1+ds/src/main.cpp [ 70%] Building CXX object CMakeFiles/program.dir/src/map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/map.cpp.o -MF CMakeFiles/program.dir/src/map.cpp.o.d -o CMakeFiles/program.dir/src/map.cpp.o -c /<>/gemmi-0.5.1+ds/src/map.cpp [ 70%] Building CXX object CMakeFiles/program.dir/src/map2sf.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/map2sf.cpp.o -MF CMakeFiles/program.dir/src/map2sf.cpp.o.d -o CMakeFiles/program.dir/src/map2sf.cpp.o -c /<>/gemmi-0.5.1+ds/src/map2sf.cpp [ 73%] Building CXX object CMakeFiles/program.dir/src/mask.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/mask.cpp.o -MF CMakeFiles/program.dir/src/mask.cpp.o.d -o CMakeFiles/program.dir/src/mask.cpp.o -c /<>/gemmi-0.5.1+ds/src/mask.cpp [ 75%] Building CXX object CMakeFiles/program.dir/src/merge.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/merge.cpp.o -MF CMakeFiles/program.dir/src/merge.cpp.o.d -o CMakeFiles/program.dir/src/merge.cpp.o -c /<>/gemmi-0.5.1+ds/src/merge.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:24, from /<>/gemmi-0.5.1+ds/src/merge.cpp:14: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 75%] Building CXX object CMakeFiles/program.dir/src/mondiff.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/mondiff.cpp.o -MF CMakeFiles/program.dir/src/mondiff.cpp.o.d -o CMakeFiles/program.dir/src/mondiff.cpp.o -c /<>/gemmi-0.5.1+ds/src/mondiff.cpp [ 78%] Building CXX object CMakeFiles/program.dir/src/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -Wno-psabi -MD -MT CMakeFiles/program.dir/src/mtz.cpp.o -MF CMakeFiles/program.dir/src/mtz.cpp.o.d -o CMakeFiles/program.dir/src/mtz.cpp.o -c /<>/gemmi-0.5.1+ds/src/mtz.cpp [ 80%] Building CXX object CMakeFiles/program.dir/src/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/mtz2cif.cpp.o -MF CMakeFiles/program.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/program.dir/src/mtz2cif.cpp.o -c /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz2cif.hpp:24, from /<>/gemmi-0.5.1+ds/src/mtz2cif.cpp:8: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 82%] Building CXX object CMakeFiles/program.dir/src/reindex.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/reindex.cpp.o -MF CMakeFiles/program.dir/src/reindex.cpp.o.d -o CMakeFiles/program.dir/src/reindex.cpp.o -c /<>/gemmi-0.5.1+ds/src/reindex.cpp [ 82%] Building CXX object CMakeFiles/program.dir/src/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/residues.cpp.o -MF CMakeFiles/program.dir/src/residues.cpp.o.d -o CMakeFiles/program.dir/src/residues.cpp.o -c /<>/gemmi-0.5.1+ds/src/residues.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /<>/gemmi-0.5.1+ds/src/residues.cpp:5: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ /usr/include/c++/11/bits/stl_heap.h: In function ‘__adjust_heap.constprop’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: the ABI of passing structure with ‘complex float’ member has changed in GCC 4.4 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^ [ 85%] Building CXX object CMakeFiles/program.dir/src/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/rmsz.cpp.o -MF CMakeFiles/program.dir/src/rmsz.cpp.o.d -o CMakeFiles/program.dir/src/rmsz.cpp.o -c /<>/gemmi-0.5.1+ds/src/rmsz.cpp [ 87%] Building CXX object CMakeFiles/program.dir/src/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/sf2map.cpp.o -MF CMakeFiles/program.dir/src/sf2map.cpp.o.d -o CMakeFiles/program.dir/src/sf2map.cpp.o -c /<>/gemmi-0.5.1+ds/src/sf2map.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/select.hpp:16, from /<>/gemmi-0.5.1+ds/src/sf2map.cpp:8: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 87%] Building CXX object CMakeFiles/program.dir/src/sfcalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/sfcalc.cpp.o -MF CMakeFiles/program.dir/src/sfcalc.cpp.o.d -o CMakeFiles/program.dir/src/sfcalc.cpp.o -c /<>/gemmi-0.5.1+ds/src/sfcalc.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/smcif.hpp:12, from /<>/gemmi-0.5.1+ds/src/sfcalc.cpp:19: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ [ 90%] Building CXX object CMakeFiles/program.dir/src/sg.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/sg.cpp.o -MF CMakeFiles/program.dir/src/sg.cpp.o.d -o CMakeFiles/program.dir/src/sg.cpp.o -c /<>/gemmi-0.5.1+ds/src/sg.cpp [ 92%] Building CXX object CMakeFiles/program.dir/src/tags.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/tags.cpp.o -MF CMakeFiles/program.dir/src/tags.cpp.o.d -o CMakeFiles/program.dir/src/tags.cpp.o -c /<>/gemmi-0.5.1+ds/src/tags.cpp [ 95%] Building CXX object CMakeFiles/program.dir/src/validate.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/validate.cpp.o -MF CMakeFiles/program.dir/src/validate.cpp.o.d -o CMakeFiles/program.dir/src/validate.cpp.o -c /<>/gemmi-0.5.1+ds/src/validate.cpp /usr/bin/strip /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/gemmi.cpython-310-x86_64-linux-gnu.so make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 95%] Built target py [ 95%] Building CXX object CMakeFiles/program.dir/src/validate_mon.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/validate_mon.cpp.o -MF CMakeFiles/program.dir/src/validate_mon.cpp.o.d -o CMakeFiles/program.dir/src/validate_mon.cpp.o -c /<>/gemmi-0.5.1+ds/src/validate_mon.cpp [ 97%] Building CXX object CMakeFiles/program.dir/src/wcn.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/wcn.cpp.o -MF CMakeFiles/program.dir/src/wcn.cpp.o.d -o CMakeFiles/program.dir/src/wcn.cpp.o -c /<>/gemmi-0.5.1+ds/src/wcn.cpp [100%] Linking CXX executable gemmi /usr/bin/cmake -E cmake_link_script CMakeFiles/program.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/program.dir/src/align.cpp.o CMakeFiles/program.dir/src/blobs.cpp.o CMakeFiles/program.dir/src/cif2mtz.cpp.o CMakeFiles/program.dir/src/cif2json.cpp.o CMakeFiles/program.dir/src/contact.cpp.o CMakeFiles/program.dir/src/contents.cpp.o CMakeFiles/program.dir/src/convert.cpp.o CMakeFiles/program.dir/src/fprime.cpp.o CMakeFiles/program.dir/src/grep.cpp.o CMakeFiles/program.dir/src/h.cpp.o CMakeFiles/program.dir/src/json2cif.cpp.o CMakeFiles/program.dir/src/main.cpp.o CMakeFiles/program.dir/src/map.cpp.o CMakeFiles/program.dir/src/map2sf.cpp.o CMakeFiles/program.dir/src/mask.cpp.o CMakeFiles/program.dir/src/merge.cpp.o CMakeFiles/program.dir/src/mondiff.cpp.o CMakeFiles/program.dir/src/mtz.cpp.o CMakeFiles/program.dir/src/mtz2cif.cpp.o CMakeFiles/program.dir/src/reindex.cpp.o CMakeFiles/program.dir/src/residues.cpp.o CMakeFiles/program.dir/src/rmsz.cpp.o CMakeFiles/program.dir/src/sf2map.cpp.o CMakeFiles/program.dir/src/sfcalc.cpp.o CMakeFiles/program.dir/src/sg.cpp.o CMakeFiles/program.dir/src/tags.cpp.o CMakeFiles/program.dir/src/validate.cpp.o CMakeFiles/program.dir/src/validate_mon.cpp.o CMakeFiles/program.dir/src/wcn.cpp.o CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o CMakeFiles/input.dir/src/input.cpp.o CMakeFiles/output.dir/src/output.cpp.o CMakeFiles/options.dir/src/options.cpp.o -o gemmi /usr/lib/x86_64-linux-gnu/libz.so /usr/include/c++/11/bits/stl_heap.h: In function ‘__adjust_heap.constprop’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: the ABI of passing structure with ‘complex float’ member has changed in GCC 4.4 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^ make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [100%] Built target program make[2]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/gemmi-0.5.1+ds' dh_auto_build -- check cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" check VERBOSE=1 make[2]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/gemmi-0.5.1+ds -B/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[3]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/gemmi-0.5.1+ds -B/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu --check-build-system 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'/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/output.dir/build'. make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target input make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/input.dir/build'. make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 2%] Built target mapcoef make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend [ 4%] Built target options make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/depend make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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/<>/gemmi-0.5.1+ds/docs/code/maybegz.cpp [ 7%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/sym.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -c /<>/gemmi-0.5.1+ds/docs/code/sym.cpp [ 9%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/hello.dir/examples/hello.cpp.o -MF CMakeFiles/hello.dir/examples/hello.cpp.o.d -o CMakeFiles/hello.dir/examples/hello.cpp.o -c /<>/gemmi-0.5.1+ds/examples/hello.cpp [ 12%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -MF CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o.d -o CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -c /<>/gemmi-0.5.1+ds/docs/code/cif_cc.cpp [ 14%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/elem.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -c /<>/gemmi-0.5.1+ds/docs/code/elem.cpp [ 17%] Building CXX object CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o -c /<>/gemmi-0.5.1+ds/docs/code/resinfo.cpp [ 17%] Building CXX object CMakeFiles/doc_example.dir/docs/code/cell.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/cell.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -c /<>/gemmi-0.5.1+ds/docs/code/cell.cpp [ 19%] Linking CXX executable doc_example /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/doc_example.dir/docs/code/sym.cpp.o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o 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CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -o doc_example2 make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 24%] Built target doc_example make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/doc_newmtz.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 24%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /<>/gemmi-0.5.1+ds/docs/code/newmtz.cpp In file included from /<>/gemmi-0.5.1+ds/include/gemmi/mtz.hpp:1135, from /<>/gemmi-0.5.1+ds/docs/code/newmtz.cpp:2: /<>/gemmi-0.5.1+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 24%] Built target hello make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/depend make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/cpptest.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 26%] Building CXX object CMakeFiles/cpptest.dir/tests/main.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/cpptest.dir/tests/main.cpp.o -MF CMakeFiles/cpptest.dir/tests/main.cpp.o.d -o CMakeFiles/cpptest.dir/tests/main.cpp.o -c /<>/gemmi-0.5.1+ds/tests/main.cpp make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 26%] Built target doc_example2 make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' cd /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu /<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu/CMakeFiles/test_disulf.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build make[5]: Entering directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 29%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /<>/gemmi-0.5.1+ds/tests/disulf.cpp In file included from /<>/gemmi-0.5.1+ds/tests/main.cpp:3: /<>/gemmi-0.5.1+ds/third_party/doctest.h:4041:47: error: size of array ‘altStackMem’ is not an integral constant-expression 4041 | static char altStackMem[4 * SIGSTKSZ]; | ^ make[5]: *** [CMakeFiles/cpptest.dir/build.make:79: CMakeFiles/cpptest.dir/tests/main.cpp.o] Error 1 make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[4]: *** [CMakeFiles/Makefile2:1052: CMakeFiles/cpptest.dir/all] Error 2 make[4]: *** Waiting for unfinished jobs.... [ 31%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o /usr/bin/c++ -I/<>/gemmi-0.5.1+ds/include -I/<>/gemmi-0.5.1+ds/third_party -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /<>/gemmi-0.5.1+ds/docs/code/mutate.cpp [ 34%] Linking CXX executable doc_newmtz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 34%] Built target doc_newmtz [ 36%] Linking CXX executable doc_maybegz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 36%] Built target doc_maybegz [ 39%] Linking CXX executable test_disulf /usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>/gemmi-0.5.1+ds=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' [ 39%] Built target test_disulf make[4]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:1327: CMakeFiles/check.dir/rule] Error 2 make[3]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' make[2]: *** [Makefile:754: check] Error 2 make[2]: Leaving directory '/<>/gemmi-0.5.1+ds/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" check VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:14: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<>/gemmi-0.5.1+ds' make: *** [debian/rules:8: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2022-01-15T06:04:04Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 199 Distribution: jammy-proposed Fail-Stage: build Host Architecture: amd64 Install-Time: 11 Job: gemmi_0.5.1+ds-1build1.dsc Machine Architecture: amd64 Package: gemmi Package-Time: 210 Source-Version: 0.5.1+ds-1build1 Space: n/a Status: attempted Version: 0.5.1+ds-1build1 -------------------------------------------------------------------------------- Finished at 2022-01-15T06:04:04Z Build needed 00:03:30, no disk space E: Build failure (dpkg-buildpackage died) Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=amd64 PACKAGEBUILD-23053203 Scanning for processes to kill in build PACKAGEBUILD-23053203