Diff of the two buildlogs: -- --- b1/build.log 2023-06-01 21:22:05.315987898 +0000 +++ b2/build.log 2023-06-01 21:44:05.830170432 +0000 @@ -1,49 +1,8 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 3 14:41:33 -12 2024 -I: pbuilder-time-stamp: 1720060893 +I: Current time: Fri Jun 2 11:22:10 +14 2023 +I: pbuilder-time-stamp: 1685654530 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel: time stamp 2025-08-04 08:27:37 is 34278354.94881786 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel.other: time stamp 2025-08-04 08:27:37 is 34278354.94848852 s in the future -tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples: time stamp 2025-08-04 08:27:37 is 34278354.94844658 s in the future -tar: ./usr/share/doc/adduser/examples: time stamp 2025-08-04 08:27:37 is 34278354.94841808 s in the future -tar: ./usr/share/doc/adduser: time stamp 2025-08-04 08:27:37 is 34278354.94839186 s in the future -tar: ./usr/share/locale/ca/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.83903556 s in the future -tar: ./usr/share/locale/cs/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.812803 s in the future -tar: ./usr/share/locale/da/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.78561448 s in the future -tar: ./usr/share/locale/de/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.75582284 s in the future -tar: ./usr/share/locale/es/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.6967768 s in the future -tar: ./usr/share/locale/eu/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.68884576 s in the future -tar: ./usr/share/locale/fr/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.60714524 s in the future -tar: ./usr/share/locale/gl/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.5965495 s in the future -tar: ./usr/share/locale/hu/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.57946558 s in the future -tar: ./usr/share/locale/it/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.5550592 s in the future -tar: ./usr/share/locale/ja/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.52544798 s in the future -tar: ./usr/share/locale/ko/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.50240004 s in the future -tar: ./usr/share/locale/nb/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.47382844 s in the future -tar: ./usr/share/locale/nl/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.44120202 s in the future -tar: ./usr/share/locale/pl/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.4131208 s in the future -tar: ./usr/share/locale/pt/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.37879818 s in the future -tar: ./usr/share/locale/pt_BR/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.3539866 s in the future -tar: ./usr/share/locale/ru/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.27931646 s in the future -tar: ./usr/share/locale/sk/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.26451394 s in the future -tar: ./usr/share/locale/sv/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.20983862 s in the future -tar: ./usr/share/locale/uk/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.11911432 s in the future -tar: ./usr/share/locale/vi/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.08771066 s in the future -tar: ./usr/share/locale/zh_CN/LC_MESSAGES: time stamp 2025-08-04 08:27:37 is 34278354.0584547 s in the future -tar: ./usr/share/man/de/man5: time stamp 2025-08-04 08:27:37 is 34278353.87258078 s in the future -tar: ./usr/share/man/fr/man5: time stamp 2025-08-04 08:27:37 is 34278353.84792862 s in the future -tar: ./usr/share/man/man5: time stamp 2025-08-04 08:27:37 is 34278353.77204492 s in the future -tar: ./usr/share/man/nl/man5: time stamp 2025-08-04 08:27:37 is 34278353.73703432 s in the future -tar: ./usr/share/man/nl/man8: time stamp 2025-08-04 08:27:37 is 34278353.7343221 s in the future -tar: ./usr/share/man/pt/man5: time stamp 2025-08-04 08:27:37 is 34278353.7186726 s in the future -tar: ./usr/share/man/pt/man8: time stamp 2025-08-04 08:27:37 is 34278353.71465018 s in the future -tar: ./usr/share/perl5/Debian: time stamp 2025-08-04 08:27:37 is 34278353.63886348 s in the future -tar: ./var/lib/dpkg/info/adduser.list: time stamp 2025-08-04 08:27:37 is 34278350.27996564 s in the future -tar: ./usr/sbin: time stamp 2025-08-04 08:27:37 is 34278349.98408252 s in the future -tar: ./usr/share/man/man8: time stamp 2025-08-04 08:27:37 is 34278349.98337676 s in the future -tar: ./usr/share/man/fr/man8: time stamp 2025-08-04 08:27:37 is 34278349.98320478 s in the future -tar: ./usr/share/man/de/man8: time stamp 2025-08-04 08:27:37 is 34278349.98309032 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem @@ -57,7 +16,7 @@ I: copying [./gemmi_0.5.7+ds.orig.tar.xz] I: copying [./gemmi_0.5.7+ds-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Oct 3 20:32:52 2022 -12 +gpgv: Signature made Tue Oct 4 22:32:52 2022 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key @@ -71,52 +30,84 @@ dpkg-source: info: applying tao-pegtl-3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/27929/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30377/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 2 11:22 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/30377/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30377/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='27929' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=30377 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.FO897zsf/pbuilderrc_lSN0 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FO897zsf/b1 --logfile b1/build.log gemmi_0.5.7+ds-2.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.FO897zsf/pbuilderrc_cWdR --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FO897zsf/b2 --logfile b2/build.log --extrapackages usrmerge gemmi_0.5.7+ds-2.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink13-arm64 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 24 04:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/27929/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 27 00:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/30377/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -265,7 +256,7 @@ Get: 89 http://deb.debian.org/debian bookworm/main arm64 python3-pybind11 all 2.10.3-1 [199 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 python3-pytest all 7.2.1-2 [236 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] -Fetched 53.3 MB in 3s (15.5 MB/s) +Fetched 53.3 MB in 1s (51.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19611 files and directories currently installed.) @@ -647,8 +638,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/gemmi-0.5.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gemmi_0.5.7+ds-2_source.changes +I: user script /srv/workspace/pbuilder/30377/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/30377/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/gemmi-0.5.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gemmi_0.5.7+ds-2_source.changes dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.5.7+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -715,51 +715,51 @@ make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-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 -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/depend make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/input.dir/DependInfo.cmake --color= -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/DependInfo.cmake --color= -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 '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/output.dir/DependInfo.cmake --color= -make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/depend make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/mapcoef.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/py.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/build make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build -make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/build -make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/build +make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build +make -f CMakeFiles/py.dir/build.make CMakeFiles/py.dir/build make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 2%] Building CXX object CMakeFiles/output.dir/src/output.cpp.o -[ 2%] Building CXX object CMakeFiles/py.dir/python/mol.cpp.o -[ 2%] Building CXX object CMakeFiles/options.dir/src/options.cpp.o +make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +[ 7%] Building CXX object CMakeFiles/py.dir/python/gemmi.cpp.o +[ 7%] Building CXX object CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o +[ 7%] Building CXX object CMakeFiles/options.dir/src/options.cpp.o +[ 7%] Building CXX object CMakeFiles/input.dir/src/input.cpp.o +[ 9%] Building CXX object CMakeFiles/py.dir/python/mol.cpp.o +[ 9%] Building CXX object CMakeFiles/output.dir/src/output.cpp.o +[ 12%] Building CXX object CMakeFiles/py.dir/python/ccp4.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/output.dir/src/output.cpp.o -MF CMakeFiles/output.dir/src/output.cpp.o.d -o CMakeFiles/output.dir/src/output.cpp.o -c /build/gemmi-0.5.7+ds/src/output.cpp +/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/gemmi.cpp.o -MF CMakeFiles/py.dir/python/gemmi.cpp.o.d -o CMakeFiles/py.dir/python/gemmi.cpp.o -c /build/gemmi-0.5.7+ds/python/gemmi.cpp +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/input.dir/src/input.cpp.o -MF CMakeFiles/input.dir/src/input.cpp.o.d -o CMakeFiles/input.dir/src/input.cpp.o -c /build/gemmi-0.5.7+ds/src/input.cpp /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/options.dir/src/options.cpp.o -MF CMakeFiles/options.dir/src/options.cpp.o.d -o CMakeFiles/options.dir/src/options.cpp.o -c /build/gemmi-0.5.7+ds/src/options.cpp +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o -MF CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o.d -o CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o -c /build/gemmi-0.5.7+ds/src/mapcoef.cpp /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/mol.cpp.o -MF CMakeFiles/py.dir/python/mol.cpp.o.d -o CMakeFiles/py.dir/python/mol.cpp.o -c /build/gemmi-0.5.7+ds/python/mol.cpp -[ 4%] Building CXX object CMakeFiles/input.dir/src/input.cpp.o -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/input.dir/src/input.cpp.o -MF CMakeFiles/input.dir/src/input.cpp.o.d -o CMakeFiles/input.dir/src/input.cpp.o -c /build/gemmi-0.5.7+ds/src/input.cpp -[ 7%] Building CXX object CMakeFiles/py.dir/python/align.cpp.o -[ 9%] Building CXX object CMakeFiles/py.dir/python/gemmi.cpp.o -/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/align.cpp.o -MF CMakeFiles/py.dir/python/align.cpp.o.d -o CMakeFiles/py.dir/python/align.cpp.o -c /build/gemmi-0.5.7+ds/python/align.cpp -/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/gemmi.cpp.o -MF CMakeFiles/py.dir/python/gemmi.cpp.o.d -o CMakeFiles/py.dir/python/gemmi.cpp.o -c /build/gemmi-0.5.7+ds/python/gemmi.cpp -[ 12%] Building CXX object CMakeFiles/py.dir/python/ccp4.cpp.o -[ 14%] Building CXX object CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/ccp4.cpp.o -MF CMakeFiles/py.dir/python/ccp4.cpp.o.d -o CMakeFiles/py.dir/python/ccp4.cpp.o -c /build/gemmi-0.5.7+ds/python/ccp4.cpp -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o -MF CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o.d -o CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o -c /build/gemmi-0.5.7+ds/src/mapcoef.cpp +[ 14%] Building CXX object CMakeFiles/py.dir/python/align.cpp.o +/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/align.cpp.o -MF CMakeFiles/py.dir/python/align.cpp.o.d -o CMakeFiles/py.dir/python/align.cpp.o -c /build/gemmi-0.5.7+ds/python/align.cpp In file included from /build/gemmi-0.5.7+ds/src/output.cpp:6: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." @@ -823,19 +823,19 @@ /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/search.cpp.o -MF CMakeFiles/py.dir/python/search.cpp.o.d -o CMakeFiles/py.dir/python/search.cpp.o -c /build/gemmi-0.5.7+ds/python/search.cpp [ 39%] Building CXX object CMakeFiles/py.dir/python/sf.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sf.cpp.o -MF CMakeFiles/py.dir/python/sf.cpp.o.d -o CMakeFiles/py.dir/python/sf.cpp.o -c /build/gemmi-0.5.7+ds/python/sf.cpp +[ 39%] Building CXX object CMakeFiles/py.dir/python/sym.cpp.o +/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sym.cpp.o -MF CMakeFiles/py.dir/python/sym.cpp.o.d -o CMakeFiles/py.dir/python/sym.cpp.o -c /build/gemmi-0.5.7+ds/python/sym.cpp [ 41%] Building CXX object CMakeFiles/program.dir/src/blobs.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/blobs.cpp.o -MF CMakeFiles/program.dir/src/blobs.cpp.o.d -o CMakeFiles/program.dir/src/blobs.cpp.o -c /build/gemmi-0.5.7+ds/src/blobs.cpp -[ 41%] Building CXX object CMakeFiles/py.dir/python/sym.cpp.o -/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/sym.cpp.o -MF CMakeFiles/py.dir/python/sym.cpp.o.d -o CMakeFiles/py.dir/python/sym.cpp.o -c /build/gemmi-0.5.7+ds/python/sym.cpp [ 43%] Building CXX object CMakeFiles/py.dir/python/topo.cpp.o /usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/topo.cpp.o -MF CMakeFiles/py.dir/python/topo.cpp.o.d -o CMakeFiles/py.dir/python/topo.cpp.o -c /build/gemmi-0.5.7+ds/python/topo.cpp -[ 46%] Building CXX object CMakeFiles/py.dir/python/unitcell.cpp.o -/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/unitcell.cpp.o -MF CMakeFiles/py.dir/python/unitcell.cpp.o.d -o CMakeFiles/py.dir/python/unitcell.cpp.o -c /build/gemmi-0.5.7+ds/python/unitcell.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/crd.hpp:13, from /build/gemmi-0.5.7+ds/python/topo.cpp:5: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ +[ 46%] Building CXX object CMakeFiles/py.dir/python/unitcell.cpp.o +/usr/bin/c++ -Dpy_EXPORTS -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -isystem /usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -std=c++17 -MD -MT CMakeFiles/py.dir/python/unitcell.cpp.o -MF CMakeFiles/py.dir/python/unitcell.cpp.o.d -o CMakeFiles/py.dir/python/unitcell.cpp.o -c /build/gemmi-0.5.7+ds/python/unitcell.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/it92.hpp:16, from /build/gemmi-0.5.7+ds/python/sf.cpp:6: /build/gemmi-0.5.7+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 5; Real = double]': @@ -911,15 +911,15 @@ | ^~~~~~~ lto-wrapper: warning: using serial compilation of 110 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information -[ 80%] Building CXX object CMakeFiles/program.dir/src/prep.cpp.o +[ 82%] Building CXX object CMakeFiles/program.dir/src/reindex.cpp.o +[ 82%] Building CXX object CMakeFiles/program.dir/src/prep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/prep.cpp.o -MF CMakeFiles/program.dir/src/prep.cpp.o.d -o CMakeFiles/program.dir/src/prep.cpp.o -c /build/gemmi-0.5.7+ds/src/prep.cpp +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/reindex.cpp.o -MF CMakeFiles/program.dir/src/reindex.cpp.o.d -o CMakeFiles/program.dir/src/reindex.cpp.o -c /build/gemmi-0.5.7+ds/src/reindex.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/crd.hpp:13, from /build/gemmi-0.5.7+ds/src/prep.cpp:7: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ -[ 82%] Building CXX object CMakeFiles/program.dir/src/reindex.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/reindex.cpp.o -MF CMakeFiles/program.dir/src/reindex.cpp.o.d -o CMakeFiles/program.dir/src/reindex.cpp.o -c /build/gemmi-0.5.7+ds/src/reindex.cpp [ 82%] Building CXX object CMakeFiles/program.dir/src/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/program.dir/src/residues.cpp.o -MF CMakeFiles/program.dir/src/residues.cpp.o.d -o CMakeFiles/program.dir/src/residues.cpp.o -c /build/gemmi-0.5.7+ds/src/residues.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/select.hpp:16, @@ -997,143 +997,150 @@ /usr/bin/cmake -E cmake_progress_start /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles 41 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_newmtz.dir/DependInfo.cmake --color= make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend +make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend +make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/depend +make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/depend +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/test_disulf.dir/DependInfo.cmake --color= -make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/check_conn.dir/DependInfo.cmake --color= -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/DependInfo.cmake --color= make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/output.dir/DependInfo.cmake --color= -make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/depend -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/mapcoef.dir/DependInfo.cmake --color= -make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/input.dir/DependInfo.cmake --color= +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/DependInfo.cmake --color= make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/output.dir/DependInfo.cmake --color= +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/cpptest.dir/DependInfo.cmake --color= +make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/hello.dir/DependInfo.cmake --color= Dependencies file "CMakeFiles/input.dir/src/input.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/input.dir/compiler_depend.internal". +Dependencies file "CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/mapcoef.dir/compiler_depend.internal". +Dependencies file "CMakeFiles/options.dir/src/options.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +Consolidate compiler generated dependencies of target options +make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build +Consolidate compiler generated dependencies of target mapcoef Consolidate compiler generated dependencies of target input make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build +make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make[5]: Nothing to be done for 'CMakeFiles/mapcoef.dir/build'. +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make -f CMakeFiles/input.dir/build.make CMakeFiles/input.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +make[5]: Nothing to be done for 'CMakeFiles/options.dir/build'. make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +Dependencies file "CMakeFiles/output.dir/src/output.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/output.dir/compiler_depend.internal". make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build -Dependencies file "CMakeFiles/options.dir/src/options.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/compiler_depend.internal". -Dependencies file "CMakeFiles/mapcoef.dir/src/mapcoef.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/mapcoef.dir/compiler_depend.internal". make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -Dependencies file "CMakeFiles/output.dir/src/output.cpp.o.d" is newer than depends file "/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/output.dir/compiler_depend.internal". -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build +[ 2%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o Consolidate compiler generated dependencies of target output -Consolidate compiler generated dependencies of target mapcoef -Consolidate compiler generated dependencies of target options -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/mapcoef.dir/build.make CMakeFiles/mapcoef.dir/build -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /build/gemmi-0.5.7+ds/tests/disulf.cpp make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 2%] Built target input -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make[5]: Nothing to be done for 'CMakeFiles/mapcoef.dir/build'. make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 4%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o make -f CMakeFiles/output.dir/build.make CMakeFiles/output.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make[5]: Nothing to be done for 'CMakeFiles/options.dir/build'. -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /build/gemmi-0.5.7+ds/tests/disulf.cpp -[ 7%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/gemmi-0.5.7+ds/examples/check_conn.cpp -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/output.dir/build'. make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 9%] Building CXX object CMakeFiles/cpptest.dir/tests/main.cpp.o -[ 12%] Built target mapcoef -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/cpptest.dir/tests/main.cpp.o -MF CMakeFiles/cpptest.dir/tests/main.cpp.o.d -o CMakeFiles/cpptest.dir/tests/main.cpp.o -c /build/gemmi-0.5.7+ds/tests/main.cpp -[ 12%] Built target options -make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend +make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/hello.dir/DependInfo.cmake --color= +[ 4%] Built target input +[ 4%] Built target options +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +[ 7%] Built target mapcoef make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/depend -[ 14%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF CMakeFiles/cpptest.dir/tests/cif.cpp.o.d -o CMakeFiles/cpptest.dir/tests/cif.cpp.o -c /build/gemmi-0.5.7+ds/tests/cif.cpp make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_example.dir/DependInfo.cmake --color= -[ 17%] Built target output -[ 17%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/depend +[ 9%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/gemmi-0.5.7+ds/examples/check_conn.cpp make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_example2.dir/DependInfo.cmake --color= -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/newmtz.cpp +[ 12%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o +[ 14%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/hello.dir/examples/hello.cpp.o -MF CMakeFiles/hello.dir/examples/hello.cpp.o.d -o CMakeFiles/hello.dir/examples/hello.cpp.o -c /build/gemmi-0.5.7+ds/examples/hello.cpp +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF CMakeFiles/cpptest.dir/tests/cif.cpp.o.d -o CMakeFiles/cpptest.dir/tests/cif.cpp.o -c /build/gemmi-0.5.7+ds/tests/cif.cpp +[ 17%] Built target output make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/build +make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/build +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +[ 19%] Building CXX object CMakeFiles/cpptest.dir/tests/main.cpp.o +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/cpptest.dir/tests/main.cpp.o -MF CMakeFiles/cpptest.dir/tests/main.cpp.o.d -o CMakeFiles/cpptest.dir/tests/main.cpp.o -c /build/gemmi-0.5.7+ds/tests/main.cpp +make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_maybegz.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/build +make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/build make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +[ 21%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.cpp.o make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build -make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 19%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.cpp.o +make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/sym.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/sym.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/sym.cpp -[ 21%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -[ 24%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o +make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +[ 24%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -MF CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o.d -o CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/cif_cc.cpp -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/hello.dir/examples/hello.cpp.o -MF CMakeFiles/hello.dir/examples/hello.cpp.o.d -o CMakeFiles/hello.dir/examples/hello.cpp.o -c /build/gemmi-0.5.7+ds/examples/hello.cpp -In file included from /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:1176, - from /build/gemmi-0.5.7+ds/docs/code/newmtz.cpp:2: -/build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] - 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." - | ^~~~~~~ +[ 26%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/maybegz.cpp In file included from /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:1176, from /build/gemmi-0.5.7+ds/include/gemmi/merge.hpp:15, from /build/gemmi-0.5.7+ds/tests/cif.cpp:93: /build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ -[ 26%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.cpp.o +[ 29%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/elem.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/elem.cpp -[ 29%] Building CXX object CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o +[ 31%] Building CXX object CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/resinfo.cpp -[ 29%] Building CXX object CMakeFiles/doc_example.dir/docs/code/cell.cpp.o +[ 31%] Building CXX object CMakeFiles/doc_example.dir/docs/code/cell.cpp.o /usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -UNDEBUG -std=c++17 -MD -MT CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/cell.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/cell.cpp -[ 31%] Linking CXX executable doc_example +[ 34%] Linking CXX executable doc_example /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_example.dir/docs/code/sym.cpp.o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o -o doc_example make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 31%] Built target doc_example -make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/depend +[ 34%] Built target doc_example +make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_maybegz.dir/DependInfo.cmake --color= +cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/doc_newmtz.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build +make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 34%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/maybegz.cpp -[ 36%] Linking CXX executable doc_newmtz -/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz +[ 34%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/newmtz.cpp +In file included from /build/gemmi-0.5.7+ds/include/gemmi/mtz.hpp:1176, + from /build/gemmi-0.5.7+ds/docs/code/newmtz.cpp:2: +/build/gemmi-0.5.7+ds/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] + 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." + | ^~~~~~~ +[ 34%] Linking CXX executable hello +/usr/bin/cmake -E cmake_link_script CMakeFiles/hello.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/hello.dir/examples/hello.cpp.o -o hello make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 36%] Built target doc_newmtz +[ 34%] Built target hello +[ 36%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o +/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/mutate.cpp +[ 36%] Linking CXX executable doc_example2 +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -o doc_example2 +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +[ 36%] Built target doc_example2 make -f CMakeFiles/program.dir/build.make CMakeFiles/program.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/program.dir/DependInfo.cmake --color= @@ -1185,18 +1192,11 @@ gemmi 0.5.7 make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' [ 92%] Built target print-version -[ 95%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -/usr/bin/c++ -I/build/gemmi-0.5.7+ds/include -I/build/gemmi-0.5.7+ds/third_party -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/gemmi-0.5.7+ds/docs/code/mutate.cpp -[ 95%] Linking CXX executable hello -/usr/bin/cmake -E cmake_link_script CMakeFiles/hello.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/hello.dir/examples/hello.cpp.o -o hello -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 95%] Built target hello -[ 95%] Linking CXX executable doc_example2 -/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -o doc_example2 +[ 95%] Linking CXX executable doc_newmtz +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 95%] Built target doc_example2 +[ 95%] Built target doc_newmtz [ 95%] Linking CXX executable cpptest /usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o -o cpptest @@ -1207,16 +1207,16 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn /usr/lib/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' [ 95%] Built target check_conn -[ 97%] Linking CXX executable test_disulf -/usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf /usr/lib/aarch64-linux-gnu/libz.so -make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[ 97%] Built target test_disulf -[100%] Linking CXX executable doc_maybegz +[ 97%] Linking CXX executable doc_maybegz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz /usr/lib/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' -[100%] Built target doc_maybegz +[ 97%] Built target doc_maybegz +[100%] Linking CXX executable test_disulf +/usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gemmi-0.5.7+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf /usr/lib/aarch64-linux-gnu/libz.so +make[5]: Leaving directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' +[100%] Built target test_disulf make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu' cd /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu /build/gemmi-0.5.7+ds/obj-aarch64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake --color= @@ -1261,7 +1261,7 @@ tests/test_twin.py .... [ 91%] tests/test_unitcell.py .............. [100%] -================= 162 passed, 9 skipped, 2 deselected in 3.97s ================= +================= 162 passed, 9 skipped, 2 deselected in 4.00s ================= make[1]: Leaving directory '/build/gemmi-0.5.7+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake @@ -1437,10 +1437,10 @@ dpkg-gencontrol: warning: Provides field of package python3-gemmi: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.5.7+ds-2_arm64.deb'. -dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.5.7+ds-2_arm64.deb'. dpkg-deb: building package 'gemmi' in '../gemmi_0.5.7+ds-2_arm64.deb'. +dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.5.7+ds-2_arm64.deb'. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.5.7+ds-2_arm64.deb'. +dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.5.7+ds-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.5.7+ds-2_arm64.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.5.7+ds-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1448,12 +1448,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/30377/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30377/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/27929 and its subdirectories -I: Current time: Wed Jul 3 15:45:04 -12 2024 -I: pbuilder-time-stamp: 1720064704 +I: removing directory /srv/workspace/pbuilder/30377 and its subdirectories +I: Current time: Fri Jun 2 11:44:04 +14 2023 +I: pbuilder-time-stamp: 1685655844