Diff of the two buildlogs: -- --- b1/build.log 2024-07-13 04:23:53.393433359 +0000 +++ b2/build.log 2024-07-13 05:00:47.927245204 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jul 12 15:42:26 -12 2024 -I: pbuilder-time-stamp: 1720842146 +I: Current time: Sat Jul 13 18:25:05 +14 2024 +I: pbuilder-time-stamp: 1720844705 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +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/10386/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/15565/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 13 04:25 /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/15565/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/15565/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='13c66dc1a559418582353ca078dec850' - 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='10386' - PS1='# ' - PS2='> ' + INVOCATION_ID=75bb6c3ce0db48cba6ffe6f9b8823599 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=15565 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.lN5d6IjF/pbuilderrc_atPj --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lN5d6IjF/b1 --logfile b1/build.log gemmi_0.6.5+ds-2.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lN5d6IjF/pbuilderrc_KpLR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lN5d6IjF/b2 --logfile b2/build.log gemmi_0.6.5+ds-2.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff4a 6.1.0-22-armmp-lpae #1 SMP Debian 6.1.94-1 (2024-06-21) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-22-arm64 #1 SMP Debian 6.1.94-1 (2024-06-21) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 22:35 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/10386/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/15565/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +259,7 @@ Get: 92 http://deb.debian.org/debian unstable/main armhf python3-pybind11 all 2.12.0-1 [208 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf python3-pytest all 8.2.2-2 [248 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf tao-pegtl-dev all 3.2.7-1 [69.4 kB] -Fetched 51.5 MB in 4s (13.4 MB/s) +Fetched 51.5 MB in 2s (30.7 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 ... 19407 files and directories currently installed.) @@ -545,8 +577,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jul 13 03:43:35 UTC 2024. -Universal Time is now: Sat Jul 13 03:43:35 UTC 2024. +Local time is now: Sat Jul 13 04:26:03 UTC 2024. +Universal Time is now: Sat Jul 13 04:26:03 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -632,7 +664,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gemmi-0.6.5+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_0.6.5+ds-2_source.changes +I: user script /srv/workspace/pbuilder/15565/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/15565/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gemmi-0.6.5+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_0.6.5+ds-2_source.changes dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.6.5+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -678,7 +714,7 @@ -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/lib/python3/dist-packages/pybind11/include (found version "2.12.0") -- Found pybind11 2.12.0: /usr/lib/python3/dist-packages/pybind11/include;/usr/include/python3.12 --- Configuring done (6.0s) +-- Configuring done (4.2s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -691,7 +727,7 @@ -- Build files have been written to: /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_auto_build -O--buildsystem=cmake - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -704,23 +740,27 @@ make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 4%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/align.cpp.o +[ 2%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/align.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/align.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/align.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/align.cpp [ 4%] Building CXX object CMakeFiles/options.dir/prog/options.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/options.dir/prog/options.cpp.o -MF CMakeFiles/options.dir/prog/options.cpp.o.d -o CMakeFiles/options.dir/prog/options.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/options.cpp -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/align.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/align.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/align.cpp [ 4%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/assembly.cpp +[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/calculate.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/calculate.cpp +[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/crd.cpp +[ 8%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/ddl.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.h:7, from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.cpp:4: @@ -735,9 +775,15 @@ 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 6%] Built target options -[ 6%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/crd.cpp +[ 8%] Built target options +[ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/eig3.cpp +[ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp:15: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/assembly.hpp:11, @@ -748,8 +794,6 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 8%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/ddl.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:359:28: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -772,6 +816,8 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -790,16 +836,19 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Connection; _Alloc = std::allocator]', - inlined from 'void gemmi::{anonymous}::finalize_expansion(gemmi::Structure&, const AssemblyMapping&, double, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/src/assembly.cpp:230:38: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::CisPep; _Alloc = std::allocator]', - inlined from 'void gemmi::{anonymous}::finalize_expansion(gemmi::Structure&, const AssemblyMapping&, double, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/src/assembly.cpp:248:28: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:14, + from /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +In file included from /usr/include/c++/13/regex:59, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ddl.hpp:11, + from /build/reproducible-path/gemmi-0.6.5+ds/src/ddl.cpp:3: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double, double}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/topo.hpp:12, @@ -817,21 +866,42 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/13/regex:59, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ddl.hpp:11, - from /build/reproducible-path/gemmi-0.6.5+ds/src/ddl.cpp:3: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double, double}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/eig3.cpp -[ 10%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp +In file included from /usr/include/c++/13/algorithm:61, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/symmetry.hpp:15, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:11: +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/bits/stl_algo.h:61: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Intensities::Refl; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Connection; _Alloc = std::allocator]', + inlined from 'void gemmi::{anonymous}::finalize_expansion(gemmi::Structure&, const AssemblyMapping&, double, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/src/assembly.cpp:230:38: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::CisPep; _Alloc = std::allocator]', + inlined from 'void gemmi::{anonymous}::finalize_expansion(gemmi::Structure&, const AssemblyMapping&, double, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/src/assembly.cpp:248:28: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double, double}; _Tp = std::pair; _Alloc = std::allocator >]', + inlined from 'gemmi::cif::{anonymous}::Validator2::Validator2(gemmi::cif::Block&, const std::map, std::__cxx11::basic_regex >&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/ddl.cpp:158:26: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:368:20, inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/neighbor.hpp:215:61: @@ -844,49 +914,15 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp:15: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double, double}; _Tp = std::pair; _Alloc = std::allocator >]', - inlined from 'gemmi::cif::{anonymous}::Validator2::Validator2(gemmi::cif::Block&, const std::map, std::__cxx11::basic_regex >&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/ddl.cpp:158:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'gemmi::add_automatic_links(Model&, Structure&, const MonLib&)::' at /build/reproducible-path/gemmi-0.6.5+ds/src/crd.cpp:119:29: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:14, - from /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -In file included from /usr/include/c++/13/algorithm:61, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/symmetry.hpp:15, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:11: -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/13/bits/stl_algo.h:61: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Intensities::Refl; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ [ 12%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/json.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/json.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp In file included from /usr/include/c++/13/vector:72, @@ -906,17 +942,17 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void gemmi::Mtz::add_base()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:233:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'gemmi::Mtz::Dataset& gemmi::Mtz::add_dataset(const std::string&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:867:23, @@ -954,8 +990,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Intensities::Refl}; _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Intensities::Refl; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void gemmi::{anonymous}::add_if_valid(gemmi::Intensities&, const gemmi::Miller&, short int, double, double)' at /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp:37:31, @@ -1029,6 +1063,8 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp [ 14%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmread_gz.cpp [ 16%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o @@ -1038,12 +1074,44 @@ /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +[ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, from /build/reproducible-path/gemmi-0.6.5+ds/src/mmread_gz.cpp:4: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, + from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +In file included from /usr/include/c++/13/algorithm:61, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:12: +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/bits/stl_algo.h:61: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Intensities::Refl; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:8, @@ -1065,6 +1133,20 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:17: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1081,16 +1163,34 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:17: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, + inlined from 'bool gemmi::validate_merged_intensities(Intensities&, Intensities&, bool, std::ostream&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:935:10: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, + inlined from 'bool gemmi::validate_merged_intensities(Intensities&, Intensities&, bool, std::ostream&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:935:10: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', @@ -1103,32 +1203,52 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void gemmi::Mtz::read_all_headers(Stream&) [with Stream = gemmi::MemoryStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:765:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::CisPep&}; _Tp = gemmi::CisPep; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void gemmi::Mtz::read_all_headers(Stream&) [with Stream = gemmi::FileStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:765:25: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/polyheur.cpp +[ 20%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::CisPep; _Alloc = std::allocator]', inlined from 'void gemmi::{anonymous}::read_prot_cis(gemmi::cif::Block&, gemmi::Structure&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp:266:25: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void gemmi::Mtz::read_all_headers(Stream&) [with Stream = gemmi::MemoryStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:765:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:15, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread_gz.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/src/mmread_gz.cpp:3: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', + inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:359:28: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', + inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:361:30: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]', @@ -1146,25 +1266,40 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void gemmi::Mtz::read_all_headers(Stream&) [with Stream = gemmi::FileStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:765:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]', inlined from 'void gemmi::{anonymous}::read_connectivity(gemmi::cif::Block&, gemmi::Structure&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp:228:32: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:15, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread_gz.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/src/mmread_gz.cpp:3: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp:5: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::BasicRefinementInfo; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ReflectionsInfo; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:349:23: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', inlined from 'gemmi::Structure gemmi::make_structure_from_block(const cif::Block&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp:528:36: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1196,50 +1331,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', - inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:359:28: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Transform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', - inlined from 'void gemmi::UnitCell::add_ncs_images_to_cs_images(const std::vector&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:361:30: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, - from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::BasicRefinementInfo; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::DiffractionInfo; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ExperimentInfo; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ReflectionsInfo; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:349:23: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1266,24 +1357,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/polyheur.cpp -In file included from /usr/include/c++/13/algorithm:61, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:12: -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/13/bits/stl_algo.h:61: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Intensities::Refl; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ +[ 20%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/resinfo.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1300,14 +1375,10 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/riding_h.cpp +[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark_200_230_240(const char*, gemmi::Metadata&, std::string*&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/remarks.hpp:504:33: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1334,6 +1405,9 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp:30:86: note: '#pragma message: Using system stb_sprintf.h, not the bundled one. It may not work.' + 30 | # pragma message("Using system stb_sprintf.h, not the bundled one. It may not work.") + | ^ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const char*&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1368,39 +1442,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, - inlined from 'bool gemmi::validate_merged_intensities(Intensities&, Intensities&, bool, std::ostream&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:935:10: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, - inlined from 'bool gemmi::validate_merged_intensities(Intensities&, Intensities&, bool, std::ostream&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:935:10: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp:5: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 20%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/resinfo.cpp -[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/riding_h.cpp +[ 25%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/topo.hpp:12, @@ -1410,6 +1453,8 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_pdb.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::{anonymous}::BondedAtom}; _Tp = gemmi::{anonymous}::BondedAtom; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::{anonymous}::BondedAtom; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void gemmi::place_hydrogens_on_all_atoms(Topo&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/riding_h.cpp:411:32: @@ -1429,28 +1474,10 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp -[ 25%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp -/build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp:30:86: note: '#pragma message: Using system stb_sprintf.h, not the bundled one. It may not work.' - 30 | # pragma message("Using system stb_sprintf.h, not the bundled one. It may not work.") - | ^ -[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_pdb.cpp [ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp In file included from /usr/include/c++/13/algorithm:60, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:8, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/to_pdb.hpp:8, - from /build/reproducible-path/gemmi-0.6.5+ds/src/to_pdb.cpp:3: -/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]': -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, - | ^~~~~~~~~ -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:8, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/to_mmcif.hpp:8, from /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp:3: /usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]': @@ -1458,6 +1485,15 @@ 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:8, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/to_pdb.hpp:8, + from /build/reproducible-path/gemmi-0.6.5+ds/src/to_pdb.cpp:3: +/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]': +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, + | ^~~~~~~~~ +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::write_pdb(const Structure&, std::ostream&, PdbWriteOptions)::]' at /usr/include/c++/13/bits/stl_algo.h:3923:28, inlined from 'bool gemmi::in_vector_f(F, const std::vector&) [with F = write_pdb(const Structure&, std::ostream&, PdbWriteOptions)::; T = NcsOp]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:247:22, @@ -1478,6 +1514,16 @@ 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', + inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/13/bits/stl_algo.h:3923:28, + inlined from 'bool std::none_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/13/bits/stl_algo.h:477:47, + inlined from 'bool std::any_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/13/bits/stl_algo.h:496:27, + inlined from 'void gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)' at /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp:626:20: +/usr/include/c++/13/bits/stl_algobase.h:2117:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2117 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2118 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::ChemComp::find_atom(const std::string&)::]' at /usr/include/c++/13/bits/stl_algo.h:3923:28, inlined from 'std::vector::iterator gemmi::ChemComp::find_atom(const std::string&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:429:24, @@ -1493,12 +1539,19 @@ 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o +/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/monlib.hpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Angle&}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, + from /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', @@ -1552,16 +1605,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', - inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/13/bits/stl_algo.h:3923:28, - inlined from 'bool std::none_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/13/bits/stl_algo.h:477:47, - inlined from 'bool std::any_of(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)::]' at /usr/include/c++/13/bits/stl_algo.h:496:27, - inlined from 'void gemmi::update_mmcif_block(const Structure&, cif::Block&, MmcifOutputGroups)' at /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp:626:20: -/usr/include/c++/13/bits/stl_algobase.h:2117:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2117 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2118 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::ChemComp::find_atom(const std::string&)::]' at /usr/include/c++/13/bits/stl_algo.h:3923:28, inlined from 'std::vector::iterator gemmi::ChemComp::find_atom(const std::string&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:429:24, @@ -1681,8 +1724,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::Restraints::Angle&}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::CisPep&}; _Tp = gemmi::CisPep; _Alloc = std::allocator]': @@ -1692,11 +1733,6 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, - from /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::ChemComp::Atom}; _Tp = gemmi::ChemComp::Atom; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1827,17 +1863,35 @@ cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_py.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build +make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' [ 33%] Building CXX object CMakeFiles/gemmi_py.dir/python/mol.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/mol.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mol.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mol.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mol.cpp [ 33%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/align.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/align.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/align.cpp -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/mol.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mol.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mol.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mol.cpp -[ 33%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o +[ 35%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o +[ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/blobs.cpp /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -MF CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/gemmi.cpp +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/blobs.cpp:4: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Blob; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const BlobCriteria&, bool):: >]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, const BlobCriteria&, bool):: >]': +/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const BlobCriteria&, bool):: >]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/prog/align.cpp:5: @@ -1866,26 +1920,6 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/align.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/align.cpp.o -MF CMakeFiles/gemmi_py.dir/python/align.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/align.cpp -[ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/blobs.cpp -In file included from /usr/include/c++/13/bits/stl_algo.h:61, - from /usr/include/c++/13/algorithm:61, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/blobs.cpp:4: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = gemmi::Blob; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const BlobCriteria&, bool):: >]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, const BlobCriteria&, bool):: >]': -/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const BlobCriteria&, bool):: >]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/grid.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/blob.hpp:13, @@ -1928,6 +1962,10 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 37%] Building CXX object CMakeFiles/gemmi_py.dir/python/align.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/align.cpp.o -MF CMakeFiles/gemmi_py.dir/python/align.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/align.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/align.cpp +[ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::Blob; _Alloc = std::allocator]', inlined from 'std::vector gemmi::find_blobs_by_flood_fill(const Grid&, const BlobCriteria&, bool)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/blob.hpp:132:26: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1953,21 +1991,16 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 37%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -MF CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, - from /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +[ 39%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2json.cpp +[ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/cifdiff.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:8, @@ -1993,31 +2026,26 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 39%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -MF CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/chemcomp.cpp -[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/cif.cpp.o -MF CMakeFiles/gemmi_py.dir/python/cif.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/cif.cpp +[ 41%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -MF CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, + from /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]', inlined from 'std::vector gemmi::as_refln_blocks(std::vector&&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/refln.hpp:152:22: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden 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Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/custom.cpp.o -MF CMakeFiles/gemmi_py.dir/python/custom.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/custom.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/custom.cpp -[ 45%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o +[ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/contact.cpp -[ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/elem.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/elem.cpp.o -MF CMakeFiles/gemmi_py.dir/python/elem.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/elem.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/elem.cpp -[ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/grid.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden 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/build/reproducible-path/gemmi-0.6.5+ds/prog/contents.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/contact.hpp:8, @@ -2050,16 +2078,12 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/contents.cpp -[ 52%] Building CXX object CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -MF CMakeFiles/gemmi_py.dir/python/hkl.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/hkl.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, - from /build/reproducible-path/gemmi-0.6.5+ds/python/hkl.cpp:9: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ +[ 45%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -MF CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/chemcomp.cpp +[ 45%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/convert.cpp +[ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/cif.cpp.o -MF CMakeFiles/gemmi_py.dir/python/cif.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/cif.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/symmetry.hpp:16, @@ -2083,10 +2107,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/convert.cpp -[ 52%] Building CXX object CMakeFiles/gemmi_py.dir/python/meta.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/meta.cpp.o -MF CMakeFiles/gemmi_py.dir/python/meta.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/meta.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/meta.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:8, @@ -2097,6 +2117,8 @@ 195 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +[ 50%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/crd.cpp In file included from /usr/include/c++/13/vector:66: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::Atom; _Alloc = std::allocator]', inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = Atom; F = remove_hydrogens(Residue&)::]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:267:10, @@ -2143,8 +2165,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS 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/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:267:10, inlined from 'bool gemmi::trim_to_alanine(Residue&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/polyheur.hpp:178:19, @@ -2153,15 +2173,24 @@ /usr/include/c++/13/bits/stl_vector.h:1566:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1566 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/crd.cpp -[ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o +[ 50%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/ecalc.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/ecalc.cpp:5: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +[ 52%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp +[ 52%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/custom.cpp.o -MF CMakeFiles/gemmi_py.dir/python/custom.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/custom.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/custom.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.h:7, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/math.hpp:9, @@ -2185,6 +2214,22 @@ 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'int fprime_main(int, char**)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp:49:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'int fprime_main(int, char**)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp:52:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/grep.cpp +[ 56%] Building CXX object CMakeFiles/gemmi_py.dir/python/elem.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/elem.cpp.o -MF CMakeFiles/gemmi_py.dir/python/elem.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/elem.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/elem.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/binner.hpp:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': @@ -2219,103 +2264,45 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 56%] Building CXX object CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mtz.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp +[ 56%] Building CXX object CMakeFiles/gemmi_py.dir/python/grid.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/grid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/grid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/grid.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/grid.cpp +[ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/h.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/h.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/h.cpp +[ 58%] Building CXX object CMakeFiles/gemmi_py.dir/python/hkl.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -MF CMakeFiles/gemmi_py.dir/python/hkl.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/hkl.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp:3: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 58%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.h:7, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'int fprime_main(int, char**)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp:49:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'int fprime_main(int, char**)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/fprime.cpp:52:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/grep.cpp -[ 62%] Building CXX object CMakeFiles/gemmi_py.dir/python/read.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/read.cpp.o 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-fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/recgrid.cpp -[ 64%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden 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/build/reproducible-path/gemmi-0.6.5+ds/python/scaling.cpp -[ 66%] Building CXX object CMakeFiles/gemmi_py.dir/python/search.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/search.cpp.o -MF CMakeFiles/gemmi_py.dir/python/search.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/search.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/search.cpp -[ 68%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o +[ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/json2cif.cpp -[ 68%] Building CXX object CMakeFiles/gemmi_py.dir/python/sf.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sf.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sf.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp -[ 68%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/main.cpp.o +[ 60%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/main.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/main.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/main.cpp -[ 70%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map.cpp.o +[ 62%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp:6: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/it92.hpp:16, - from /build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:6: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:60:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:83:20: required from here -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 73 | std::pair calculate_with_derivative(float r) const { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]' -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:60:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::Neutron92; pybind11::module = pybind11::module_]' -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:85:25: required from here -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 48 | std::pair calculate_with_derivative(Real r) const { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 1]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:149:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, float>; Table = gemmi::IT92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:128:32: required from 'void gemmi::DensityCalculator::add_c_contribution_to_grid(const gemmi::Atom&, float) [with Table = gemmi::IT92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:47:40: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' -/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:83:20: required from here -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 73 | std::pair calculate_with_derivative(float r) const { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o +[ 62%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/map2sf.cpp -[ 72%] Building CXX object CMakeFiles/gemmi_py.dir/python/sym.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sym.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sym.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sym.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/sym.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/map2sf.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 72%] Building CXX object CMakeFiles/gemmi_py.dir/python/topo.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/topo.cpp.o -MF CMakeFiles/gemmi_py.dir/python/topo.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/topo.cpp +[ 62%] Building CXX object CMakeFiles/gemmi_py.dir/python/meta.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/meta.cpp.o -MF CMakeFiles/gemmi_py.dir/python/meta.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/meta.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/meta.cpp +[ 64%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mapcoef.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/mapcoef.cpp:11: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/grid.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/prog/map2sf.cpp:9: @@ -2335,12 +2322,10 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -MF CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/unitcell.cpp -[ 77%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mapcoef.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/mapcoef.cpp:11: +[ 66%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp:5: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ @@ -2358,16 +2343,7 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object CMakeFiles/gemmi_py.dir/python/write.cpp.o -/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/write.cpp.o -MF CMakeFiles/gemmi_py.dir/python/write.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/write.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/write.cpp -[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp:5: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o +[ 66%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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/build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp In file included from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:8: @@ -2396,14 +2369,6 @@ /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:63, - from /usr/include/c++/13/set:62, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp:7: -/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&):: >]': -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, - | ^~~~~~~~~ -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/asudata.hpp:10, @@ -2420,9 +2385,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&, const AtomId&, const AtomId&):: >]': -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2431,13 +2393,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp:8: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {int}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2446,20 +2401,75 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::ChemComp::Atom}; _Tp = gemmi::ChemComp::Atom; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:63, + from /usr/include/c++/13/set:62, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp:7: +/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&):: >]': +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, + | ^~~~~~~~~ +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&, const AtomId&, const AtomId&):: >]': +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp:8: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Plane}; _Tp = gemmi::Restraints::Plane; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::ChemComp::Atom}; _Tp = gemmi::ChemComp::Atom; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Bond}; _Tp = gemmi::Restraints::Bond; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +[ 68%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/monlib_opt.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Angle}; _Tp = gemmi::Restraints::Angle; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]', + inlined from 'std::vector gemmi::as_refln_blocks(std::vector&&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/refln.hpp:152:22: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', + inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:84:23, + inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::GzStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:283:48: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', + inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::GzStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:351:24: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', + inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:84:23, + inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:283:48: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', + inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:351:24: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::ChemComp::Atom}; _Tp = gemmi::ChemComp::Atom; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::ChemComp::Atom; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:597:23: @@ -2491,33 +2501,14 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::cif::Block}; _Tp = gemmi::ReflnBlock; _Alloc = std::allocator]', - inlined from 'std::vector gemmi::as_refln_blocks(std::vector&&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/refln.hpp:152:22: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', - inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:84:23, - inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::GzStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:283:48: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', - inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::GzStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:351:24: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', - inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:84:23, - inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:283:48: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', - inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:351:24: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred(const AtomId&, const AtomId&):: >]', inlined from '_IIter std::find_if(_IIter, _IIter, _Predicate) [with _IIter = __gnu_cxx::__normal_iterator >; _Predicate = gemmi::Restraints::find_bond(const AtomId&, const AtomId&)::]' at /usr/include/c++/13/bits/stl_algo.h:3923:28, inlined from 'std::vector::iterator gemmi::Restraints::find_bond(const T&, const T&) [with T = AtomId]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:154:24, @@ -2562,24 +2553,6 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2118 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/monlib_opt.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void gemmi::Intensities::sort()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:95:26, @@ -2604,13 +2577,8 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o +[ 70%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp:8: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ In file included from /usr/include/c++/13/map:62, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/monlib.hpp:9, from /build/reproducible-path/gemmi-0.6.5+ds/prog/monlib_opt.h:5, @@ -2619,6 +2587,19 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, gemmi::EnerLib::Atom>, std::_Select1st, gemmi::EnerLib::Atom> >, std::less >, std::allocator, gemmi::EnerLib::Atom> > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp:8: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +[ 70%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp:8: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In file included from /usr/include/c++/13/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&, gemmi::EnerLib::Atom}; _Key = std::__cxx11::basic_string; _Tp = gemmi::EnerLib::Atom; _Compare = std::less >; _Alloc = std::allocator, gemmi::EnerLib::Atom> >]', inlined from 'std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Alloc>::rebind >::other>::iterator, bool> std::map<_Key, _Tp, _Compare, _Alloc>::emplace(_Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&, gemmi::EnerLib::Atom}; _Key = std::__cxx11::basic_string; _Tp = gemmi::EnerLib::Atom; _Compare = std::less >; _Alloc = std::allocator, gemmi::EnerLib::Atom> >]' at /usr/include/c++/13/bits/stl_map.h:601:22, @@ -2628,16 +2609,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 641 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp +[ 72%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp:8: + from /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp:9: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -lto-wrapper: warning: using serial compilation of 114 LTRANS jobs -lto-wrapper: note: see the '-flto' option documentation for more information +[ 75%] Building CXX object CMakeFiles/gemmi_py.dir/python/monlib.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -MF CMakeFiles/gemmi_py.dir/python/monlib.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/monlib.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:17: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': @@ -2672,6 +2652,26 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:17: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:349:23: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:84:23, inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::GzStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:283:48: @@ -2683,8 +2683,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:84:23, inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::FileStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:283:48: @@ -2704,33 +2702,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp:9: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ -[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/residues.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:17: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:349:23: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2739,31 +2710,17 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:14, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:13, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/residues.cpp:5: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o +[ 75%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/residues.cpp +[ 77%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/rmsz.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void gemmi::impl::parse_cid(const std::string&, gemmi::Selection&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:516:38: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o +[ 79%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp:6: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp In file included from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:9: @@ -2772,50 +2729,28 @@ 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:9: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:14, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:13, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/residues.cpp:5: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:16: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/it92.hpp:16, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:14: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:149:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<4, 1, float>; Table = gemmi::IT92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:122:32: required from 'void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::IT92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:196:11: required from 'void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:201:5: required from 'void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:243:36: required from 'void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::IT92; Real = float]' -/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:690:23: required from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::IT92]' -/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:812:43: required from here -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 73 | std::pair calculate_with_derivative(float r) const { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:149:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, double>; Table = gemmi::Neutron92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:122:32: required from 'void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::Neutron92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:196:11: required from 'void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:201:5: required from 'void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]' -/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:243:36: required from 'void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::Neutron92; Real = float]' -/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:690:23: required from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::Neutron92]' -/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:817:49: required from here -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 48 | std::pair calculate_with_derivative(Real r) const { - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:19: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp: In function 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]': -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void gemmi::impl::parse_cid(const std::string&, gemmi::Selection&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:516:38: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 79%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Selection::AtomInequality}; _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Selection::AtomInequality; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void gemmi::impl::parse_cid(const std::string&, gemmi::Selection&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/select.hpp:516:38: @@ -2855,10 +2790,57 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o +[ 79%] Building CXX object CMakeFiles/gemmi_py.dir/python/mtz.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mtz.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:9: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp:3: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sg.cpp -[ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o +[ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/tags.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/it92.hpp:16, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:14: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:149:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<4, 1, float>; Table = gemmi::IT92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:122:32: required from 'void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::IT92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:196:11: required from 'void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:201:5: required from 'void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:243:36: required from 'void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::IT92; Real = float]' +/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:690:23: required from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::IT92]' +/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:812:43: required from here +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 73 | std::pair calculate_with_derivative(float r) const { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:149:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, double>; Table = gemmi::Neutron92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:122:32: required from 'void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::Neutron92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:196:11: required from 'void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:201:5: required from 'void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:243:36: required from 'void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::SolventMasker&, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::Neutron92; Real = float]' +/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:690:23: required from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::Neutron92]' +/build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:817:49: required from here +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 48 | std::pair calculate_with_derivative(Real r) const { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:19: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp: In function 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 19 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/assembly.hpp:11, @@ -2913,6 +2895,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate_mon.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::SmallStructure::Site; _Alloc = std::allocator]', inlined from 'gemmi::SmallStructure gemmi::make_small_structure_from_block(const cif::Block&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/smcif.hpp:74:23: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -2985,6 +2969,8 @@ /usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object CMakeFiles/gemmi_py.dir/python/read.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/read.cpp.o -MF CMakeFiles/gemmi_py.dir/python/read.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/read.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/read.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Scaling::Point}; _Tp = gemmi::Scaling::Point; _Alloc = std::allocator::Point>]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::Point, std::allocator::Point> >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3034,18 +3020,11 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate.cpp -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void gemmi::StructureFactorCalculator::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/sfcalc.hpp:37:31, - inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/sfcalc.hpp:131:37, - inlined from 'void {anonymous}::print_structure_factors_sm(const gemmi::SmallStructure&, gemmi::StructureFactorCalculator
&, bool, double, bool, const RefFile&) [with Table = gemmi::Neutron92]' at /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:392:62, - inlined from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::Neutron92]' at /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:697:33: -/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1037 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate_mon.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/pdb.hpp:23, + from /build/reproducible-path/gemmi-0.6.5+ds/python/read.cpp:7: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:8, @@ -3063,8 +3042,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Restraints::Torsion}; _Tp = gemmi::Restraints::Torsion; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 97%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::ChemComp::Atom}; _Tp = gemmi::ChemComp::Atom; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::ChemComp::Atom; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'gemmi::ChemComp gemmi::make_chemcomp_from_block(const cif::Block&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp.hpp:597:23: @@ -3096,10 +3073,27 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp +[ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o +/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp:8: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void gemmi::StructureFactorCalculator
::set_stol2_and_scattering_factors(const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/sfcalc.hpp:37:31, + inlined from 'std::complex gemmi::StructureFactorCalculator
::calculate_sf_from_small_structure(const gemmi::SmallStructure&, const gemmi::Miller&) [with Table = gemmi::Neutron92]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/sfcalc.hpp:131:37, + inlined from 'void {anonymous}::print_structure_factors_sm(const gemmi::SmallStructure&, gemmi::StructureFactorCalculator
&, bool, double, bool, const RefFile&) [with Table = gemmi::Neutron92]' at /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:392:62, + inlined from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::Neutron92]' at /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:697:33: +/usr/include/c++/13/bits/stl_vector.h:1037:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1037 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/neighbor.hpp:9, from /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp:5: @@ -3111,8 +3105,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[100%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:368:20, @@ -3126,15 +3118,26 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:14, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/gz.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp:7: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 195 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp:8: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ +In file included from /usr/include/c++/13/vector:66: +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', + inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = XdsAscii::Refl; F = XdsAscii::eliminate_batchmin(int)::]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:267:10, + inlined from 'void gemmi::XdsAscii::eliminate_batchmin(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:192:21: +/usr/include/c++/13/bits/stl_vector.h:1566:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1566 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from '{anonymous}::Result {anonymous}::test_bfactor_models(gemmi::Structure&, const Params&)' at /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp:237:26, @@ -3148,22 +3151,6 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:14, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/gz.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp:7: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 195 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/13/vector:66: -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = gemmi::XdsAscii::Refl; _Alloc = std::allocator]', - inlined from 'void gemmi::vector_remove_if(std::vector&, F&&) [with T = XdsAscii::Refl; F = XdsAscii::eliminate_batchmin(int)::]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:267:10, - inlined from 'void gemmi::XdsAscii::eliminate_batchmin(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:192:21: -/usr/include/c++/13/bits/stl_vector.h:1566:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1566 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3180,12 +3167,16 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +[ 91%] Building CXX object CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/recgrid.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void gemmi::Mtz::add_base()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:233:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object CMakeFiles/gemmi_py.dir/python/scaling.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -MF CMakeFiles/gemmi_py.dir/python/scaling.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/scaling.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {int&}; _Tp = gemmi::XdsAscii::Iset; _Alloc = std::allocator]', inlined from 'gemmi::XdsAscii::Iset& gemmi::XdsAscii::find_or_add_iset(int)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:84:23, inlined from 'void gemmi::XdsAscii::read_stream(Stream&&, const std::string&) [with Stream = gemmi::GzStream]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:283:48: @@ -3221,11 +3212,56 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[100%] Linking CXX executable gemmi +[ 91%] Linking CXX executable gemmi /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_prog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/gemmi_prog.dir/prog/align.cpp.o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o CMakeFiles/options.dir/prog/options.cpp.o -o gemmi libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so +[ 93%] Building CXX object CMakeFiles/gemmi_py.dir/python/search.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/search.cpp.o -MF CMakeFiles/gemmi_py.dir/python/search.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/search.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/search.cpp make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[100%] Built target gemmi_prog +[ 93%] Built target gemmi_prog +[ 93%] Building CXX object CMakeFiles/gemmi_py.dir/python/sf.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sf.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sf.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp +[ 95%] Building CXX object CMakeFiles/gemmi_py.dir/python/sym.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/sym.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sym.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sym.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/sym.cpp +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/it92.hpp:16, + from /build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:6: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:60:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:83:20: required from here +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 73 | std::pair calculate_with_derivative(float r) const { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]' +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:60:36: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::Neutron92; pybind11::module = pybind11::module_]' +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:85:25: required from here +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:48:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 48 | std::pair calculate_with_derivative(Real r) const { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 1]': +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:19:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:136:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:149:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, float>; Table = gemmi::IT92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/dencalc.hpp:128:32: required from 'void gemmi::DensityCalculator::add_c_contribution_to_grid(const gemmi::Atom&, float) [with Table = gemmi::IT92; GReal = float]' +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:47:40: required from 'void add_dencalc(pybind11::module&, const char*) [with Table = gemmi::IT92; pybind11::module = pybind11::module_]' +/build/reproducible-path/gemmi-0.6.5+ds/python/sf.cpp:83:20: required from here +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/formfact.hpp:73:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 73 | std::pair calculate_with_derivative(float r) const { + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 95%] Building CXX object CMakeFiles/gemmi_py.dir/python/topo.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/topo.cpp.o -MF CMakeFiles/gemmi_py.dir/python/topo.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/topo.cpp +[ 97%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o +/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem 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Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/cpptest.dir/DependInfo.cmake "--color=" Dependencies file "CMakeFiles/options.dir/prog/options.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/options.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/align.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target options Dependencies file "CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -Dependencies file "CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build +make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build +Dependencies file "CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/build Dependencies file "CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make[5]: Nothing to be done for 'CMakeFiles/options.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' Dependencies file "CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target options Dependencies file "CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build +make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build Dependencies file "CMakeFiles/gemmi_cpp.dir/src/json.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make[5]: Nothing to be done for 'CMakeFiles/options.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' Dependencies file "CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' Dependencies file "CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +[ 0%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o +/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -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/reproducible-path/gemmi-0.6.5+ds/docs/code/cif_cc.cpp Dependencies file "CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +[ 2%] Built target options Dependencies file "CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend Dependencies file "CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -[ 0%] Building CXX object CMakeFiles/cpptest.dir/tests/main.cpp.o Dependencies file "CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". +[ 2%] Building CXX object CMakeFiles/cpptest.dir/tests/main.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -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/reproducible-path/gemmi-0.6.5+ds/tests/main.cpp Dependencies file "CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_cpp.dir/compiler_depend.internal". -[ 2%] Built target options -make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/hello.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 4%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -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/reproducible-path/gemmi-0.6.5+ds/examples/hello.cpp Consolidate compiler generated dependencies of target gemmi_cpp make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/build +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' make[5]: Nothing to be done for 'CMakeFiles/gemmi_cpp.dir/build'. make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 4%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o +/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -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/reproducible-path/gemmi-0.6.5+ds/examples/hello.cpp [ 33%] Built target gemmi_cpp make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' @@ -3333,27 +3377,18 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro 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 CMakeFiles/doc_example.dir/src/resinfo.cpp.o -o doc_example make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' [ 41%] Built target doc_example -make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/depend +make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/doc_example2.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/check_conn.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/build +make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 41%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -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/reproducible-path/gemmi-0.6.5+ds/docs/code/cif_cc.cpp +[ 41%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o +/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/examples/check_conn.cpp [ 41%] 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/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/hello.dir/examples/hello.cpp.o -o hello make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 41%] Built target hello -make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/depend -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/doc_maybegz.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 43%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/doctest/doctest.h:3169, from /build/reproducible-path/gemmi-0.6.5+ds/tests/main.cpp:3: @@ -3361,6 +3396,10 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 41%] Built target hello +make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/depend +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) 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/build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp:2: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ -[ 45%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o -/usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF CMakeFiles/cpptest.dir/tests/cif.cpp.o.d -o CMakeFiles/cpptest.dir/tests/cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/tests/cif.cpp -[ 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'/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 93%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o +/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -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/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp In file included from /usr/include/c++/13/vector:72, from 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[with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': @@ -3410,11 +3512,48 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void gemmi::Mtz::add_base()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:233:23: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'gemmi::Mtz::Dataset& gemmi::Mtz::add_dataset(const std::string&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:867:23, + inlined from 'int main()' at /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp:9:18: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 95%] Built target doc_newmtz +make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/depend +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/print-version.dir/DependInfo.cmake "--color=" +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/build +make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 95%] gemmi --version +cd /build/reproducible-path/gemmi-0.6.5+ds && /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/gemmi --version +gemmi 0.6.5 +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 95%] Built target print-version +[ 95%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o +/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/mutate.cpp +[ 95%] Linking CXX executable cpptest +/usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.dir/link.txt --verbose=1 +In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, + from /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp:11: +/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] + 37 | typedef std::unique_ptr fileptr_t; + | ^ In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:8, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp_xyz.hpp:9, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:8: + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/neighbor.hpp:9, + from /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3431,23 +3570,12 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void gemmi::Mtz::add_base()' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:233:23: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Mtz::Dataset}; _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::Mtz::Dataset; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'gemmi::Mtz::Dataset& gemmi::Mtz::add_dataset(const std::string&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:867:23, - inlined from 'int main()' at /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp:9:18: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::BasicRefinementInfo; _Alloc = std::allocator]': @@ -3460,58 +3588,37 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::ReflectionsInfo; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 50%] 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/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 50%] Built target doc_newmtz -make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/test_disulf.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 52%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -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/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:349:23: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', + inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:368:20, + inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/neighbor.hpp:215:61: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::CisPep&}; _Tp = gemmi::CisPep; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] 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/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o -o cpptest -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::CisPep&}; _Tp = gemmi::CisPep; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 52%] Built target cpptest -make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/check_conn.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build -make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 52%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/examples/check_conn.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::Assembly::Operator; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3520,12 +3627,15 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, - from /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp:11: -/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] - 37 | typedef std::unique_ptr fileptr_t; - | ^ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {BondInfo}; _Tp = BondInfo; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BondInfo}; _Tp = BondInfo; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o -o cpptest /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3534,6 +3644,16 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[ 95%] Built target cpptest +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) 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[with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const char*&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3582,92 +3693,16 @@ 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) 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'/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 95%] gemmi --version -cd /build/reproducible-path/gemmi-0.6.5+ds && /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/gemmi --version -gemmi 0.6.5 -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 95%] Built target print-version -[ 95%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/mutate.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/neighbor.hpp:9, - from /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp:8: + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/iterator.hpp:10, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cifdoc.hpp:8, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/chemcomp_xyz.hpp:9, + from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:8: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3684,12 +3719,25 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::FTransform&}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]', + inlined from 'void gemmi::pdb_impl::read_remark3_line(const char*, gemmi::Metadata&, std::string*&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/remarks.hpp:325:39: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]', + inlined from 'void gemmi::pdb_impl::read_remark3_line(const char*, gemmi::Metadata&, std::string*&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/remarks.hpp:381:35: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::BasicRefinementInfo; _Alloc = std::allocator]', + inlined from 'void gemmi::pdb_impl::read_remark3_line(const char*, gemmi::Metadata&, std::string*&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/remarks.hpp:385:49: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::TlsGroup; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::RefinementInfo; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {}; _Tp = gemmi::BasicRefinementInfo; _Alloc = std::allocator]': @@ -3704,36 +3752,26 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::FTransform}; _Tp = gemmi::FTransform; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'void gemmi::UnitCell::set_cell_images_from_spacegroup(const gemmi::SpaceGroup*)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:349:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::FTransform; _Alloc = std::allocator]', - inlined from 'std::vector gemmi::UnitCell::get_ncs_transforms() const' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/unitcell.hpp:368:20, - inlined from 'void gemmi::NeighborSearch::set_bounding_cell(const gemmi::UnitCell&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/neighbor.hpp:215:61: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[ 97%] Built target doc_maybegz /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::CisPep&}; _Tp = gemmi::CisPep; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Connection&}; _Tp = gemmi::Connection; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gemmi::CisPep&}; _Tp = gemmi::CisPep; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gemmi::Atom&}; _Tp = gemmi::Atom; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -3746,14 +3784,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {BondInfo}; _Tp = BondInfo; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BondInfo}; _Tp = BondInfo; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gemmi::NcsOp}; _Tp = gemmi::NcsOp; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3762,14 +3792,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {}; _Tp = gemmi::CrystalInfo; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::read_remark_200_230_240(const char*, gemmi::Metadata&, std::string*&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/remarks.hpp:504:33: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3790,11 +3812,20 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gemmi::CisPep; _Alloc = std::allocator]', inlined from 'void gemmi::pdb_impl::process_conn(gemmi::Structure&, const std::vector >&)' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/pdb.hpp:212:27: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::__cxx11::basic_string, std::allocator >}; _Tp = gemmi::Assembly; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const char*&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3809,8 +3840,8 @@ 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::__cxx11::basic_string, std::allocator >&}; _Tp = gemmi::RefinementInfo::Restr; _Alloc = std::allocator]', - inlined from 'T& gemmi::impl::find_or_add(std::vector&, const std::string&) [with T = gemmi::RefinementInfo::Restr]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:43:19, - inlined from 'T& gemmi::impl::find_or_add(std::vector&, const std::string&) [with T = gemmi::RefinementInfo::Restr]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:40:4: + inlined from 'T& gemmi::impl::find_or_add(std::vector&, const std::string&) [with T = gemmi::RefinementInfo::Restr]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:43:19, + inlined from 'T& gemmi::impl::find_or_add(std::vector&, const std::string&) [with T = gemmi::RefinementInfo::Restr]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/model.hpp:40:4: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3829,11 +3860,16 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[100%] Linking CXX executable test_disulf +[ 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/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' -[100%] Built target test_disulf +[ 97%] Built target test_disulf +[100%] Linking CXX executable doc_maybegz +/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fexcess-precision=fast -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz libgemmi_cpp.a /usr/lib/arm-linux-gnueabihf/libz.so +make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' +[100%] Built target doc_maybegz make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf/CMakeFiles/check.dir/DependInfo.cmake "--color=" @@ -3843,7 +3879,7 @@ /usr/bin/ctest -C None Test project /build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf Start 1: cpptest -1/1 Test #1: cpptest .......................... Passed 0.01 sec +1/1 Test #1: cpptest .......................... Passed 0.02 sec 100% tests passed, 0 tests failed out of 1 @@ -3876,13 +3912,13 @@ SKIPPED [1] tests/test_seq.py:146: BioPython not installed. SKIPPED [1] tests/test_seq.py:105: BioPython not installed. SKIPPED [1] tests/test_seq.py:114: BioPython not installed. -172 passed, 17 skipped, 2 deselected in 4.61s +172 passed, 17 skipped, 2 deselected in 7.06s make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/gemmi-0.6.5\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/reproducible-path/gemmi-0.6.5\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -3894,110 +3930,110 @@ -- Install configuration: "None" -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/bin/gemmi -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqid.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bessel.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/utf.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_pdb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cellred.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/small.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/symmetry.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/grid.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cifdoc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/it92.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/calculate.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/smcif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/select.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/eig3.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif2mtz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/model.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/binner.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/topo.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/intensit.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ccp4.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dirwalk.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/polyheur.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb_id.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/modify.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neutron92.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/assembly.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/span.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/twin.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/elem.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/c4322.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fileutil.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/small.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/contact.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_json.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread_gz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cellred.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/reciproc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/json.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/metadata.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cifdoc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atof.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ddl.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/solmask.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/tinydir.h +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/version.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/recgrid.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asudata.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dencalc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/monlib.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/math.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fstream.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/json.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/numb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/riding_h.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/refln.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_json.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asumask.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fail.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/stats.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sfcalc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/resinfo.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/crd.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/solmask.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/qcp.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/iterator.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neighbor.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmdb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/gz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/addends.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/polyheur.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/blob.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/numb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/it92.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/elem.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqalign.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neutron92.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqtools.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fprime.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_cif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/qcp.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/math.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asudata.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/align.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atox.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/floodfill.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/input.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/unitcell.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/serialize.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ccp4.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asumask.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/util.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fprime.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/c4322.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/refln.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bond_idx.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmdb.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/scaling.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/select.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/levmar.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/input.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fourier.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/grid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/monlib.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/crd.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dirwalk.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/util.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_map.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/smcif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sprintf.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_cif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/remarks.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/riding_h.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/eig3.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fstream.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/addends.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/span.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/contact.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ddl.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/interop.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bond_idx.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/binner.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_cif.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqalign.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fileutil.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/metadata.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atox.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atof.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/align.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqtools.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/model.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bessel.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/formfact.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/twin.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/stats.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dencalc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/modify.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb_id.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_pdb.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/unitcell.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fail.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/enumstr.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fourier.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/gz.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/assembly.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/serialize.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sfcalc.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/utf.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif2mtz.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ecalc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/reciproc.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread_gz.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/remarks.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_map.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/levmar.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/formfact.hpp --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/topo.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/version.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/iterator.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/blob.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/calculate.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/recgrid.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neighbor.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/libgemmi_cpp.a -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/gemmi/gemmi-targets.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/gemmi/gemmi-targets-none.cmake @@ -4005,30 +4041,30 @@ -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/gemmi/gemmi-config-version.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi.cpython-312-arm-linux-gnueabihf.so -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/weight.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/map2mtz.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_plot.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtz_i_sigi.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskdiff.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/long_geom.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_gather.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/monomers.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/from_json.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/sub_ccd.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/map2mtz.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/simple_search.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/cif_i_sigi.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtz_i_sigi.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/weight.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_gi.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_subgraph.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_gather.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/long_geom.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/multiproc.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_plot.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/sub_ccd.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/cif_i_sigi.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/refln-stats.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_gi.py --- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/from_json.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/hello.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py +-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-arm-linux-gnueabihf' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake @@ -4069,9 +4105,9 @@ 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-dev' in '../gemmi-dev_0.6.5+ds-2_armhf.deb'. -dpkg-deb: building package 'gemmi' in '../gemmi_0.6.5+ds-2_armhf.deb'. dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.6.5+ds-2_armhf.deb'. +dpkg-deb: building package 'gemmi' in '../gemmi_0.6.5+ds-2_armhf.deb'. +dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.6.5+ds-2_armhf.deb'. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.5+ds-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.6.5+ds-2_armhf.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.6.5+ds-2_armhf.changes @@ -4080,12 +4116,14 @@ 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/15565/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/15565/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/10386 and its subdirectories -I: Current time: Fri Jul 12 16:23:48 -12 2024 -I: pbuilder-time-stamp: 1720844628 +I: removing directory /srv/workspace/pbuilder/15565 and its subdirectories +I: Current time: Sat Jul 13 19:00:39 +14 2024 +I: pbuilder-time-stamp: 1720846839