Diff of the two buildlogs: -- --- b1/build.log 2025-10-25 03:01:01.822512175 +0000 +++ b2/build.log 2025-10-25 03:17:40.707879045 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 24 14:29:06 -12 2025 -I: pbuilder-time-stamp: 1761359346 +I: Current time: Fri Nov 27 23:24:52 +14 2026 +I: pbuilder-time-stamp: 1795771492 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -54,53 +54,85 @@ dpkg-source: info: applying 0029-Fix-Python-syntax-warnings.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1804204/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2671576/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 27 09:25 /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/2671576/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2671576/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='9b3b68944b774c66a825cfc260101950' - 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='1804204' - PS1='# ' - PS2='> ' + INVOCATION_ID=c5c643555ead4b28acb0f27d3268e6dd + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2671576 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.U3YQgZw6/pbuilderrc_Wdrd --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.U3YQgZw6/b1 --logfile b1/build.log cctbx_2025.2+ds2+~3.23.0+ds1-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.U3YQgZw6/pbuilderrc_PF6Z --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.U3YQgZw6/b2 --logfile b2/build.log cctbx_2025.2+ds2+~3.23.0+ds1-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1804204/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2671576/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -757,7 +789,7 @@ Get: 514 http://deb.debian.org/debian unstable/main arm64 python3-tqdm all 4.67.1-6 [90.9 kB] Get: 515 http://deb.debian.org/debian unstable/main arm64 python3-wxgtk4.0 arm64 4.2.3+dfsg-2 [6910 kB] Get: 516 http://deb.debian.org/debian unstable/main arm64 scons all 4.8.1+dfsg-1 [548 kB] -Fetched 347 MB in 4s (78.8 MB/s) +Fetched 347 MB in 2s (140 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (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 ... 19962 files and directories currently installed.) @@ -2419,8 +2451,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Oct 25 02:29:56 UTC 2025. -Universal Time is now: Sat Oct 25 02:29:56 UTC 2025. +Local time is now: Fri Nov 27 09:26:17 UTC 2026. +Universal Time is now: Fri Nov 27 09:26:17 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-5) ... @@ -2883,7 +2915,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/ && 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 > ../cctbx_2025.2+ds2+~3.23.0+ds1-1_source.changes +I: user script /srv/workspace/pbuilder/2671576/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2671576/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/ && 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 > ../cctbx_2025.2+ds2+~3.23.0+ds1-1_source.changes dpkg-buildpackage: info: source package cctbx dpkg-buildpackage: info: source version 2025.2+ds2+~3.23.0+ds1-1 dpkg-buildpackage: info: source distribution unstable @@ -7193,18 +7229,8 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/eltbx/henke.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/henke.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/libiotbx_xplor.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libiotbx_xplor.so.0 iotbx/xplor/map_reader.o iotbx/xplor/map_writer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm g++ -o cctbx/eltbx/henke_tables_01_12.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/henke_tables_01_12.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/libiotbx_xplor.so.0.0.1' - 'lib/libiotbx_xplor.so.0'->'lib/libiotbx_xplor.so.0.0.1' - 'lib/libiotbx_xplor.so'->'lib/libiotbx_xplor.so.0.0.1' g++ -o cctbx/eltbx/henke_tables_13_24.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/henke_tables_13_24.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/eltbx/henke_tables_25_36.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/henke_tables_25_36.cpp @@ -7215,13 +7241,23 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/eltbx/henke_tables_61_72.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/henke_tables_61_72.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/libiotbx_xplor.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libiotbx_xplor.so.0 iotbx/xplor/map_reader.o iotbx/xplor/map_writer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm g++ -o cctbx/eltbx/henke_tables_73_84.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/henke_tables_73_84.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/eltbx/henke_tables_85_92.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/henke_tables_85_92.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/eltbx/icsd_radii.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/icsd_radii.cpp -g++ -o cctbx/eltbx/covalent_radii.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/covalent_radii.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.socc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/libiotbx_xplor.so.0.0.1' + 'lib/libiotbx_xplor.so.0'->'lib/libiotbx_xplor.so.0.0.1' + 'lib/libiotbx_xplor.so'->'lib/libiotbx_xplor.so.0.0.1' +g++ -o cctbx/eltbx/covalent_radii.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/covalent_radii.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/eltbx/neutron.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/neutron.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ @@ -7238,8 +7274,8 @@ g++ -o cctbx/eltbx/sasaki_tables_49_60.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_49_60.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/eltbx/sasaki_tables_61_72.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_61_72.cpp -g++ -o cctbx/eltbx/sasaki_tables_73_82.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_73_82.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/eltbx/sasaki_tables_73_82.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include cctbx/eltbx/sasaki_tables_73_82.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/eltbx/tiny_pse.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/tiny_pse.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ @@ -7254,8 +7290,8 @@ g++ -o cctbx/miller/bins.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/bins.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/miller/index_generator.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/index_generator.cpp -g++ -o cctbx/miller/index_span.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/index_span.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/miller/index_span.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/index_span.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/miller/match_bijvoet_mates.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/match_bijvoet_mates.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ @@ -7292,11 +7328,11 @@ g++ -o cctbx/sgtbx/row_echelon_solve.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/row_echelon_solve.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/rt_mx.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/rt_mx.cpp -g++ -o cctbx/sgtbx/select_generators.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/select_generators.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/sgtbx/select_generators.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/select_generators.cpp g++ -o cctbx/sgtbx/seminvariant.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/seminvariant.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/site_symmetry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/space_group.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/space_group.cpp @@ -7306,9 +7342,9 @@ g++ -o cctbx/sgtbx/symbols.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/symbols.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/tensor_rank_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensor_rank_2.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/tr_group.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tr_group.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/tr_vec.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tr_vec.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/utils.cpp @@ -7320,19 +7356,17 @@ g++ -o cctbx/sgtbx/reference_settings/matrix_group_code_table.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/reference_settings/matrix_group_code_table.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/reference_settings/normalizer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/reference_settings/normalizer.cpp -g++ -o cctbx/sgtbx/reference_settings/wyckoff.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/reference_settings/wyckoff.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/sgtbx/reference_settings/wyckoff.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/reference_settings/wyckoff.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/uctbx/uctbx.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx/uctbx.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/uctbx/spoil_optimization.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx/spoil_optimization.cpp -g++ -o cctbx/uctbx/crystal_orientation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx/crystal_orientation.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/uctbx/crystal_orientation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx/crystal_orientation.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o omptbx/stubs.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/omptbx/stubs.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o boost_adaptbx/graph/breadth_first_search_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/libomptbx.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libomptbx.so.0 omptbx/stubs.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -7345,6 +7379,8 @@ Create symlinks for: 'lib/libomptbx.so.0.0.1' 'lib/libomptbx.so.0'->'lib/libomptbx.so.0.0.1' 'lib/libomptbx.so'->'lib/libomptbx.so.0.0.1' +g++ -o boost_adaptbx/graph/breadth_first_search_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o boost_adaptbx/graph/clustering_algorithm_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/clustering_algorithm_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o boost_adaptbx/graph/connected_component_algorithm_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/connected_component_algorithm_ext.cpp @@ -7388,7 +7424,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/clustering_algorithm_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7407,7 +7443,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/connected_component_algorithm_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_structure_comparison_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7424,7 +7460,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/connected_component_algorithm_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7441,7 +7477,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/metric_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7458,7 +7494,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_structure_comparison_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/clustering_algorithm_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7475,7 +7511,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/maximum_clique_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/min_cut_max_flow_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7492,7 +7528,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/utility_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/breadth_first_search_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7509,7 +7545,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/min_cut_max_flow_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/utility_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7526,7 +7562,7 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object.hpp:9, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/graph_type.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/metric_ext.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/graph/maximum_clique_ext.cpp:1: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -7542,9 +7578,9 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o boost_adaptbx/tuple_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/boost_adaptbx/tuple_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o boost_adaptbx/tests/tst_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread boost_adaptbx/tests/tst_optional_copy.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system g++ -o cbflib_adaptbx/detectors/boost_python/cbflib_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include/hdf5/serial -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx/detectors/boost_python/cbflib_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o boost_adaptbx/tests/tst_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread boost_adaptbx/tests/tst_optional_copy.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system g++ -o cbflib_adaptbx/detectors/buffer_based_service.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include/hdf5/serial -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx/detectors/buffer_based_service.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cbflib_adaptbx/detectors/cbf_adaptor.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include/hdf5/serial -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx/detectors/cbf_adaptor.cpp @@ -7570,9 +7606,9 @@ g++ -o cctbx/adp_restraints/fixed_u_eq_adp_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/adp_restraints/fixed_u_eq_adp_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/adp_restraints/isotropic_adp_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/adp_restraints/isotropic_adp_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/adp_restraints/rigid_bond_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/adp_restraints/rigid_bond_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/adp_restraints/rigu_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/adp_restraints/rigu_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/adptbx/boost_python/adptbx_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/adptbx/boost_python/adptbx_ext.cpp @@ -7597,10 +7633,6 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/boost_python/statistics_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/boost_python/statistics_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o cctbx/covariance/boost_python/covariance_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/covariance/boost_python/covariance_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o cctbx/crystal/asu_clusters_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/asu_clusters_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/libcctbx_sgtbx_asu.so.0.0.1 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread -shared -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -Wl,-soname=libcctbx_sgtbx_asu.so.0 cctbx/sgtbx/direct_space_asu/proto/cut.o cctbx/sgtbx/direct_space_asu/proto/reference_table.o cctbx/sgtbx/direct_space_asu/proto/direct_space_asu.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lm /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -7609,6 +7641,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o cctbx/covariance/boost_python/covariance_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/covariance/boost_python/covariance_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/crystal/asu_clusters_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/asu_clusters_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/libcctbx_sgtbx_asu.so.0.0.1' 'lib/libcctbx_sgtbx_asu.so.0'->'lib/libcctbx_sgtbx_asu.so.0.0.1' 'lib/libcctbx_sgtbx_asu.so'->'lib/libcctbx_sgtbx_asu.so.0.0.1' @@ -7619,12 +7655,12 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o cctbx/crystal/close_packing_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/close_packing_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/libasymmetric_map.so.0.0.1' 'lib/libasymmetric_map.so.0'->'lib/libasymmetric_map.so.0.0.1' 'lib/libasymmetric_map.so'->'lib/libasymmetric_map.so.0.0.1' g++ -o bin/cctbx_blobs -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/maptbx/blobs_cmd.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lasymmetric_map -liotbx_xplor -lcctbx_sgtbx_asu -lcctbx -lomptbx -lm -g++ -o cctbx/crystal/close_packing_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/close_packing_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/crystal/coordination_sequences_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/coordination_sequences_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/crystal/crystal_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/crystal_ext.cpp @@ -7703,27 +7739,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ - 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here - 203 | new tensor_rank_3_constraints_t(matrices_.const_ref(), 1, true)); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 185 | for (int j = 0; j < tensor_t::size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ - 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here - 214 | new tensor_rank_4_constraints_t(matrices_.const_ref(), 1, true)); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 185 | for (int j = 0; j < tensor_t::size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/restraints.h:6, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_similarity.h:6, @@ -7732,47 +7747,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = cctbx::geometry_restraints::angle_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ - 130 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 131 | w_t, - | ~~~~ - 132 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 133 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/angle_bpl.cpp:75:65: required from here - 75 | scitbx::af::boost_python::shared_wrapper::wrap( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ - 76 | "shared_angle_proxy") - | ~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_similarity.h: In constructor ‘cctbx::geometry_restraints::bond_similarity::bond_similarity(const scitbx::af::const_ref, scitbx::af::trivial_accessor>&, const cctbx::geometry_restraints::bond_similarity_proxy&)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_similarity.h:84:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 84 | for(int i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/angle_bpl.cpp:11: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = cctbx::geometry_restraints::bond_similarity_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = cctbx::geometry_restraints::angle_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ 130 | scitbx::boost_python::container_conversions::from_python_sequence< | ^~~~~~~~~~~~~~~~~~~~~ 131 | w_t, @@ -7859,13 +7822,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 133 | ::variable_capacity_policy>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:55:44: required from here - 54 | scitbx::af::boost_python::shared_wrapper< - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 55 | bond_similarity_proxy, rir>::wrap( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ - 56 | "shared_bond_similarity_proxy"); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/angle_bpl.cpp:75:65: required from here + 75 | scitbx::af::boost_python::shared_wrapper::wrap( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ + 76 | "shared_angle_proxy") + | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ @@ -7880,12 +7841,12 @@ from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:31, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:12, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:11: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:9: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = cctbx::geometry_restraints::chirality_proxy; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = cctbx::geometry_restraints::bond_similarity_proxy; GetitemReturnValuePolicy = boost::python::return_internal_reference<>; std::string = std::__cxx11::basic_string]’ 130 | scitbx::boost_python::container_conversions::from_python_sequence< | ^~~~~~~~~~~~~~~~~~~~~ 131 | w_t, @@ -7894,14 +7855,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 133 | ::variable_capacity_policy>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:75:60: required from here - 75 | scitbx::af::boost_python::shared_wrapper::wrap( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ - 76 | "shared_chirality_proxy") - | ~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_similarity_bpl.cpp:55:44: required from here + 54 | scitbx::af::boost_python::shared_wrapper< + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 55 | bond_similarity_proxy, rir>::wrap( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ + 56 | "shared_bond_similarity_proxy"); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/wyckoff.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/direct_space_asu.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/asu_cache.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_misc.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_bpl.cpp:14: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i::convertible(PyObject*) [with ContainerType = scitbx::af::shared, 2> >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared, 2> >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, @@ -7925,6 +7899,14 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/restraints.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/chirality.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:13: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -7946,17 +7928,62 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/wyckoff.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/direct_space_asu.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/asu_cache.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_sorted.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_sorted_bpl.cpp:9: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ + 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here + 203 | new tensor_rank_3_constraints_t(matrices_.const_ref(), 1, true)); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 185 | for (int j = 0; j < tensor_t::size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ + 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here + 214 | new tensor_rank_4_constraints_t(matrices_.const_ref(), 1, true)); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 185 | for (int j = 0; j < tensor_t::size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~ +g++ -o cctbx/geometry_restraints/geometry_restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/geometry_restraints_ext.cpp +In file included from /usr/include/c++/15/cassert:46, + from /usr/include/boost/move/detail/type_traits.hpp:33, + from /usr/include/boost/move/traits.hpp:31, + from /usr/include/boost/move/utility.hpp:30, + from /usr/include/boost/optional/optional.hpp:59, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:31, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:12, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:11: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = cctbx::geometry_restraints::chirality_proxy; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ + 130 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 131 | w_t, + | ~~~~ + 132 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 133 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/chirality_bpl.cpp:75:60: required from here + 75 | scitbx::af::boost_python::shared_wrapper::wrap( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ + 76 | "shared_chirality_proxy") + | ~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/c++/15/cassert:46, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -8032,6 +8059,19 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/wyckoff.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/direct_space_asu.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/asu_cache.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_sorted.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/bond_sorted_bpl.cpp:9: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -8069,9 +8109,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/direct_space_asu.h:869:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, std::allocator > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 869 | for(int i_sym=0; i_sym::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i cctbx::geometry_restraints::shared_proxy_remove(const scitbx::af::const_ref&, const scitbx::af::const_ref&) [with ProxyType = dihedral_proxy]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/dihedral_bpl.cpp:110:17: required from here @@ -8143,36 +8181,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -g++ -o cctbx/geometry_restraints/nonbonded_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/nonbonded_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/geometry_restraints/nonbonded_sorted_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/nonbonded_sorted_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o cctbx/geometry_restraints/parallelity_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/parallelity_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/memory:71, - from /usr/include/boost/config/no_tr1/memory.hpp:21, - from /usr/include/boost/get_pointer.hpp:14, - from /usr/include/boost/python/object/pointer_holder.hpp:11, - from /usr/include/boost/python/to_python_indirect.hpp:10, - from /usr/include/boost/python/converter/arg_to_python.hpp:10, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object.hpp:9, - from /usr/include/boost/python/tuple.hpp:10, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/shared_wrapper_pickle.hpp:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/angle_bpl.cpp:2: -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ declared here - 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ^~~~~~~~~~~~~ -g++ -o cctbx/geometry_restraints/planarity_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/planarity_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/wyckoff.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/direct_space_asu.h:4, @@ -8256,6 +8266,30 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +g++ -o cctbx/geometry_restraints/parallelity_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/parallelity_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/memory:71, + from /usr/include/boost/config/no_tr1/memory.hpp:21, + from /usr/include/boost/get_pointer.hpp:14, + from /usr/include/boost/python/object/pointer_holder.hpp:11, + from /usr/include/boost/python/to_python_indirect.hpp:10, + from /usr/include/boost/python/converter/arg_to_python.hpp:10, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/object.hpp:9, + from /usr/include/boost/python/tuple.hpp:10, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/shared_wrapper_pickle.hpp:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/angle_bpl.cpp:2: +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ declared here + 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/wyckoff.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/direct_space_asu.h:4, @@ -8267,6 +8301,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -8401,8 +8437,8 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/math/time_trigonometry -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/math/time_trigonometry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_timer -lm g++ -o cctbx/miller/boost_python/amplitude_normalisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/boost_python/amplitude_normalisation.cpp -g++ -o cctbx/miller/boost_python/asu.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/boost_python/asu.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/miller/boost_python/asu.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/boost_python/asu.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/miller/boost_python/bins.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/boost_python/bins.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ @@ -8441,9 +8477,9 @@ g++ -o cctbx/multipolar/aspherical_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/multipolar/aspherical_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/boost_python/brick.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/boost_python/brick.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/boost_python/change_of_basis.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/boost_python/change_of_basis.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/boost_python/find_affine.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/boost_python/find_affine.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o cctbx/sgtbx/boost_python/lattice_symmetry.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/boost_python/lattice_symmetry.cpp @@ -8517,66 +8553,23 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/curvatures_simple.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/curvatures_simple.cpp:3: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/gradients_direct.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/each_hkl_gradients_direct.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/each_hkl_gradients_direct.cpp:3: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ - 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here - 203 | new tensor_rank_3_constraints_t(matrices_.const_ref(), 1, true)); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 185 | for (int j = 0; j < tensor_t::size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ - 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here - 214 | new tensor_rank_4_constraints_t(matrices_.const_ref(), 1, true)); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 185 | for (int j = 0; j < tensor_t::size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx.h:11, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/change_of_basis_op.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tr_group.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/space_group.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_constraints.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:4: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In instantiation of ‘scitbx::af::small_plain::small_plain(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:50:33: required from ‘scitbx::af::small::small(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’ - 50 | : base_class(first, last) - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/xray_scattering.h:155:11: required from ‘cctbx::eltbx::xray_scattering::gaussian cctbx::eltbx::xray_scattering::base::fetch() const [with long unsigned int N = 4]’ - 155 | small_t(entry_->a, entry_->a+N), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:192:40: required from here - 191 | ugs[ui] = eltbx::xray_scattering::it1992( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 192 | pair->first, exact).fetch(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:69:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] - 69 | if (N < last - first) throw_range_error(); - | ~~^~~~~~~~~~~~~~ +g++ -o cctbx/xray/boost_python/gradient_flags.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/gradient_flags.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/gradients_direct.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/each_hkl_gradients_direct.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/each_hkl_gradients_direct.cpp:3: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/curvatures_simple.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/curvatures_simple.cpp:3: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -8620,21 +8613,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:69:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 69 | if (N < last - first) throw_range_error(); | ~~^~~~~~~~~~~~~~ -g++ -o cctbx/xray/boost_python/gradients_direct.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/gradients_direct.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o cctbx/xray/boost_python/grouped_data.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/grouped_data.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o cctbx/xray/boost_python/minimization.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/minimization.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/sampling_base.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/fast_gradients.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/fast_gradients.cpp:3: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -8720,6 +8698,10 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +g++ -o cctbx/xray/boost_python/gradients_direct.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/gradients_direct.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/xray/boost_python/grouped_data.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/grouped_data.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/f_model.h: In instantiation of ‘cctbx::xray::f_model_core_data::f_model_core_data cctbx::xray::f_model_core_data::f_model_core_data::select(const scitbx::af::const_ref&) const [with FloatType = double]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/f_model_bpl.cpp:174:32: required from here 174 | .def("select", &w_t::select) @@ -8732,6 +8714,62 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/f_model.h:732:10: note: in expansion of macro ‘CCTBX_ASSERT’ 732 | CCTBX_ASSERT( iselection[ii]::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ + 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here + 203 | new tensor_rank_3_constraints_t(matrices_.const_ref(), 1, true)); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 185 | for (int j = 0; j < tensor_t::size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ + 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here + 214 | new tensor_rank_4_constraints_t(matrices_.const_ref(), 1, true)); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 185 | for (int j = 0; j < tensor_t::size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx.h:11, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/change_of_basis_op.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tr_group.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/space_group.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_constraints.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:4: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In instantiation of ‘scitbx::af::small_plain::small_plain(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:50:33: required from ‘scitbx::af::small::small(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’ + 50 | : base_class(first, last) + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/xray_scattering.h:155:11: required from ‘cctbx::eltbx::xray_scattering::gaussian cctbx::eltbx::xray_scattering::base::fetch() const [with long unsigned int N = 4]’ + 155 | small_t(entry_->a, entry_->a+N), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:192:40: required from here + 191 | ugs[ui] = eltbx::xray_scattering::it1992( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 192 | pair->first, exact).fetch(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:69:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] + 69 | if (N < last - first) throw_range_error(); + | ~~^~~~~~~~~~~~~~ +g++ -o cctbx/xray/boost_python/parameter_map.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/parameter_map.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/gradients_direct.h:4, @@ -8790,8 +8828,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -8815,8 +8851,6 @@ | ~~^~~~~~~~~~~~~~~~~~ g++ -o cctbx/xray/boost_python/sampled_model_density.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/sampled_model_density.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o cctbx/xray/boost_python/sampling_base.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/sampling_base.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/match_indices.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/lookup_utils.h:11, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/grouped_data.h:14, @@ -8859,8 +8893,6 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -o cctbx/xray/boost_python/scatterer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/grouped_data.h: In instantiation of ‘FloatType cctbx::xray::grouped_data::merger::bic() [with FloatType = double]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/grouped_data.cpp:68:29: required from here 68 | .def("bic", &w_t::bic) @@ -9084,18 +9116,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/grouped_data.h:167:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 167 | for (int ii=0; ii::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i::small_plain(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:50:33: required from ‘scitbx::af::small::small(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’ - 50 | : base_class(first, last) - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/xray_scattering.h:155:11: required from ‘cctbx::eltbx::xray_scattering::gaussian cctbx::eltbx::xray_scattering::base::fetch() const [with long unsigned int N = 4]’ - 155 | small_t(entry_->a, entry_->a+N), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:192:40: required from here - 191 | ugs[ui] = eltbx::xray_scattering::it1992( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 192 | pair->first, exact).fetch(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:69:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] - 69 | if (N < last - first) throw_range_error(); - | ~~^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:6: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ - 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here - 203 | new tensor_rank_3_constraints_t(matrices_.const_ref(), 1, true)); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 185 | for (int j = 0; j < tensor_t::size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ - 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here - 214 | new tensor_rank_4_constraints_t(matrices_.const_ref(), 1, true)); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 185 | for (int j = 0; j < tensor_t::size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/sampling_base.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/sampling_base.cpp:3: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i::init_scatterer_part(const scitbx::af::const_ref&) [with XRayScattererType = cctbx::xray::scatterer<>]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/parameter_map.h:54:7: required from ‘cctbx::xray::parameter_map::parameter_map(const scitbx::af::const_ref&) [with XRayScattererType = cctbx::xray::scatterer<>]’ @@ -9241,13 +9213,29 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/parameter_map.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref, scitbx::af::trivial_accessor>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for(int i_sc=0; i_sc < scatterers.size(); ++i_sc) { | ~~~~~^~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/xray/boost_python/scatterer_flags.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer_flags.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer.cpp:3: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/sampling_base.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/sampled_model_density.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/sampled_model_density.cpp:3: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -9269,20 +9257,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h: In instantiation of ‘static void cctbx::xray::inelastic_form_factors::set(const scitbx::af::ref&, float, bool) [with ScattererType = cctbx::xray::scatterer<>; TableType = cctbx::eltbx::henke::table]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer.cpp:349:54: required from here - 349 | inelastic_form_factors::set, - | ^~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h:426:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 426 | for (int i=0; i < scatterers.size(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h: In instantiation of ‘static void cctbx::xray::inelastic_form_factors::set(const scitbx::af::ref&, float, bool) [with ScattererType = cctbx::xray::scatterer<>; TableType = cctbx::eltbx::sasaki::table]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer.cpp:353:55: required from here - 353 | inelastic_form_factors::set, - | ^~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h:426:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 426 | for (int i=0; i < scatterers.size(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx.h:11, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/change_of_basis_op.h:6, @@ -9326,10 +9300,78 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ -g++ -o cctbx/xray/boost_python/sigmaa.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/sigmaa.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx.h:11, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/change_of_basis_op.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tr_group.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/space_group.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_constraints.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:4: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In instantiation of ‘scitbx::af::small_plain::small_plain(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:50:33: required from ‘scitbx::af::small::small(const OtherElementType*, const OtherElementType*) [with OtherElementType = float; ElementType = double; long unsigned int N = 10]’ + 50 | : base_class(first, last) + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/eltbx/xray_scattering.h:155:11: required from ‘cctbx::eltbx::xray_scattering::gaussian cctbx::eltbx::xray_scattering::base::fetch() const [with long unsigned int N = 4]’ + 155 | small_t(entry_->a, entry_->a+N), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:192:40: required from here + 191 | ugs[ui] = eltbx::xray_scattering::it1992( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 192 | pair->first, exact).fetch(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:69:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] + 69 | if (N < last - first) throw_range_error(); + | ~~^~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer.cpp:3: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i::set(const scitbx::af::ref&, float, bool) [with ScattererType = cctbx::xray::scatterer<>; TableType = cctbx::eltbx::henke::table]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer.cpp:349:54: required from here + 349 | inelastic_form_factors::set, + | ^~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h:426:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 426 | for (int i=0; i < scatterers.size(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h: In instantiation of ‘static void cctbx::xray::inelastic_form_factors::set(const scitbx::af::ref&, float, bool) [with ScattererType = cctbx::xray::scatterer<>; TableType = cctbx::eltbx::sasaki::table]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer.cpp:353:55: required from here + 353 | inelastic_form_factors::set, + | ^~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_utils.h:426:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 426 | for (int i=0; i < scatterers.size(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~ +g++ -o cctbx/xray/boost_python/structure_factors_simple.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/structure_factors_simple.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:6: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ + 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here + 203 | new tensor_rank_3_constraints_t(matrices_.const_ref(), 1, true)); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 185 | for (int j = 0; j < tensor_t::size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ + 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here + 214 | new tensor_rank_4_constraints_t(matrices_.const_ref(), 1, true)); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 185 | for (int j = 0; j < tensor_t::size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~ +g++ -o cctbx/xray/boost_python/targets.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/targets.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/xray/boost_python/twin_components.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/twin_components.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scatterer_flags.cpp:7: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: @@ -9343,6 +9385,29 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 49 | std::auto_ptr + | ^~~~~~~~ +In file included from /usr/include/c++/15/memory:80, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/misc.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/vec3.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sym_mat3.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_flags.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:4: +/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here + 58 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp: In static member function ‘static std::auto_ptr cctbx::xray::boost_python::{anonymous}::scattering_type_registry_wrappers::constructor_for_pickle(const boost::python::dict&, const boost::python::list&, const cctbx::xray::scattering_type_registry::unique_counts_t&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp:55:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 55 | std::auto_ptr self(new w_t); + | ^~~~~~~~ +/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here + 58 | template class auto_ptr; + | ^~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:6: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -9392,31 +9457,13 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -g++ -o cctbx/xray/boost_python/structure_factors_simple.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/structure_factors_simple.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp: At global scope: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp:49:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 49 | std::auto_ptr - | ^~~~~~~~ -In file included from /usr/include/c++/15/memory:80, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/misc.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/vec3.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sym_mat3.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer_flags.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:4: -/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here - 58 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp: In static member function ‘static std::auto_ptr cctbx::xray::boost_python::{anonymous}::scattering_type_registry_wrappers::constructor_for_pickle(const boost::python::dict&, const boost::python::list&, const cctbx::xray::scattering_type_registry::unique_counts_t&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/scattering_type_registry.cpp:55:12: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 55 | std::auto_ptr self(new w_t); - | ^~~~~~~~ -/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here - 58 | template class auto_ptr; - | ^~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/sigmaa.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/sigmaa.cpp:8: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -9438,7 +9485,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ -g++ -o cctbx/xray/boost_python/targets.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/targets.cpp +g++ -o cctbx/xray/boost_python/twin_targets.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/twin_targets.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/uctbx.h:11, @@ -9462,21 +9509,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:69:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 69 | if (N < last - first) throw_range_error(); | ~~^~~~~~~~~~~~~~ -g++ -o cctbx/xray/boost_python/twin_components.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/twin_components.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o cctbx/xray/boost_python/twin_targets.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/twin_targets.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o cctbx/xray/boost_python/xray_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/xray_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/sigmaa.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/sigmaa.cpp:8: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -9498,6 +9530,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ +g++ -o cctbx/xray/boost_python/xray_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/boost_python/xray_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o cctbx/xray/observations/boost_python/observations.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/observations/boost_python/observations.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scattering_type_registry.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/structure_factors_direct.h:4, @@ -9506,8 +9542,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -9606,6 +9636,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:69:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 69 | if (N < last - first) throw_range_error(); | ~~^~~~~~~~~~~~~~ +g++ -o cctbx/xray/observations/boost_python/observations_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/observations/boost_python/observations_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_ptr.hpp:25, from /usr/include/boost/shared_ptr.hpp:17, @@ -9665,6 +9697,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +g++ -o cctbx/xray/targets/shelxl_wght_ls_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/targets/shelxl_wght_ls_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o chiltbx/handle_test.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/chiltbx/handle_test.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o chiltbx/handle_test -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread chiltbx/handle_test.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system g++ -o cma_es/cma/cmaes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cma_es/cma/cmaes.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ @@ -10094,6 +10130,32 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/quadrature.h:546:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 546 | for (int ii=0;ii >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 40 | if (pos < 0 || pos >= command_line_args.buffer.size()) { @@ -10120,8 +10184,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/read.hpp:653:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 653 | if (iw+1 != ed.size()) { | ~~~~~^~~~~~~~~~~~ -g++ -o cma_es/cma_es_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cma_es/cma_es_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/variant.hpp:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/major_types.hpp:7: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/equivalence.hpp: In member function ‘void fem::utils::equivalence::array_alignment::infer_diffs0_from_diff_matrix()’: @@ -10133,32 +10195,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/write.hpp:704:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 704 | while (pos < internal_file_len) { | ~~~~^~~~~~~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/boost_python/compression.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc: In function ‘unsigned int dxtbx::boost_python::cbf_decompress(const char*, std::size_t, int*, std::size_t)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc:124:50: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 124 | while ((j < packed_sz) && ((values - original) < values_sz)) { - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc: In function ‘void dxtbx::boost_python::rod_TY6_decompress(int*, const char*, const char*, int, int)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc:204:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] - 204 | for (size_t iy = 0; iy < slow; iy++) { - | ~~~^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc:225:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] - 225 | for (int k = 0; k < nblock; k++) { - | ~~^~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc:251:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] - 251 | for (int j = 0; j < nbit; j++) { - | ~~^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc:258:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] - 258 | for (int j = 0; j < BLOCKSIZE; j++) { - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/compression.cc:279:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] - 279 | for (int i = 0; i < nrest; i++) { - | ~~^~~~~~~ -g++ -o dxtbx/src/dxtbx/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o dxtbx/src/dxtbx/boost_python/flumpy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o dxtbx/src/dxtbx/boost_python/imageset_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.cpp @@ -10169,6 +10205,9 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o dxtbx/src/dxtbx/masking/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/boost_python/ext.cc cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.cpp:10:1: warning: ‘typedef’ was ignored in this declaration + 10 | typedef struct cbf_handle_struct; + | ^~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, @@ -10190,297 +10229,8 @@ 220 | for (std::size_t x = upper_left[0]; x < lower_right[0]; x++) { g++ -o dxtbx/src/dxtbx/model/boost_python/beam.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.cpp:10:1: warning: ‘typedef’ was ignored in this declaration - 10 | typedef struct cbf_handle_struct; - | ^~~~~~~ g++ -o dxtbx/src/dxtbx/model/boost_python/crystal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = bool; grid = scitbx::af::versa >]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:247:31: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ - 247 | return get_buffer_specific(obj); - | ~~~~~~~~~~~~~~~~~~~^~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here - 254 | return get_buffer(obj.ptr()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/boost_python/ext.cc:3: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘std::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = bool]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:125:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = bool]’ - 125 | .def("__init__", make_constructor(&make_image_from_tuple)) - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:141:24: required from here - 141 | image_wrapper("ImageBool"); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:51:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 51 | for (std::size_t i = 0; i < boost::python::len(data); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:551:18: warning: ‘scitbx::vec3 dxtbx::model::Beam::direction_’ [-Wreorder] - 551 | vec3 direction_; - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:93:5: warning: when initialized here [-Wreorder] - 93 | Beam() - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] - 552 | double divergence_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:126:5: warning: when initialized here [-Wreorder] - 126 | Beam(vec3 direction, double wavelength) - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] - 552 | double divergence_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:165:5: warning: when initialized here [-Wreorder] - 165 | Beam(vec3 direction, - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double, scitbx::vec3, double, double, double, dxtbx::model::Probe)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] - 552 | double divergence_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:193:5: warning: when initialized here [-Wreorder] - 193 | Beam(vec3 direction, - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double, scitbx::vec3, double, double, double, dxtbx::model::Probe, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] - 552 | double divergence_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:227:5: warning: when initialized here [-Wreorder] - 227 | Beam(vec3 direction, - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘std::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:125:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = int]’ - 125 | .def("__init__", make_constructor(&make_image_from_tuple)) - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:142:23: required from here - 142 | image_wrapper("ImageInt"); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:51:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 51 | for (std::size_t i = 0; i < boost::python::len(data); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In member function ‘virtual scitbx::af::shared > dxtbx::model::PolychromaticBeam::get_s0_at_scan_points() const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:52: warning: left operand of comma operator has no effect [-Wunused-value] - 760 | return scitbx::af::shared >(1, (0., 0., 0.)); - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] - 760 | return scitbx::af::shared >(1, (0., 0., 0.)); - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘std::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:125:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = double]’ - 125 | .def("__init__", make_constructor(&make_image_from_tuple)) - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:143:26: required from here - 143 | image_wrapper("ImageDouble"); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:51:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 51 | for (std::size_t i = 0; i < boost::python::len(data); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = long unsigned int; grid = scitbx::af::versa >]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:247:31: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ - 247 | return get_buffer_specific(obj); - | ~~~~~~~~~~~~~~~~~~~^~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ - 249 | return get_buffer(ptr); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here - 254 | return get_buffer(obj.ptr()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:17: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:288:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:289:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 289 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:328:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 328 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:329:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 329 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:408:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 408 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:409:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 409 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:449:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘static void dxtbx::format::boost_python::ImagePickleSuite::setstate(dxtbx::format::Image&, boost::python::tuple) [with T = bool]’: -/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ - 345 | &PickleSuiteType::setstate, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:134:18: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = bool]’ - 122 | class_(name) - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 123 | .def(init()) - | ~~~~~~~~~~~~~~~~~~~~~~~ - 124 | .def("__init__", make_constructor(&make_image_from_flex)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 125 | .def("__init__", make_constructor(&make_image_from_tuple)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 126 | .def("__getitem__", &image_type::tile) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 127 | .def("tile", &image_type::tile) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 128 | .def("tile_names", &image_type::tile_names) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 129 | .def("n_tiles", &image_type::n_tiles) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 130 | .def("empty", &image_type::empty) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 131 | .def("append", &image_type::push_back) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 132 | .def("__len__", &image_type::n_tiles) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 133 | .def("__iter__", range(&image_type::begin, &image_type::end)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 134 | .def_pickle(ImagePickleSuite()); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:141:24: required from here - 141 | image_wrapper("ImageBool"); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:98:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 98 | for (std::size_t i = 0; i < boost::python::len(tile_list); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h: In member function ‘void dxtbx::model::Panel::apply_untrusted_rectangle_mask(scitbx::af::ref >) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:435:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 435 | for (std::size_t y = y0; y < y1; ++y) { - | ~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 436 | for (std::size_t x = x0; x < x1; ++x) { - | ~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘static void dxtbx::format::boost_python::ImagePickleSuite::setstate(dxtbx::format::Image&, boost::python::tuple) [with T = int]’: -/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ - 345 | &PickleSuiteType::setstate, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:134:18: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = int]’ - 122 | class_(name) - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 123 | .def(init()) - | ~~~~~~~~~~~~~~~~~~~~~~~ - 124 | .def("__init__", make_constructor(&make_image_from_flex)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 125 | .def("__init__", make_constructor(&make_image_from_tuple)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 126 | .def("__getitem__", &image_type::tile) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 127 | .def("tile", &image_type::tile) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 128 | .def("tile_names", &image_type::tile_names) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 129 | .def("n_tiles", &image_type::n_tiles) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 130 | .def("empty", &image_type::empty) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 131 | .def("append", &image_type::push_back) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 132 | .def("__len__", &image_type::n_tiles) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 133 | .def("__iter__", range(&image_type::begin, &image_type::end)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 134 | .def_pickle(ImagePickleSuite()); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:142:23: required from here - 142 | image_wrapper("ImageInt"); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:98:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 98 | for (std::size_t i = 0; i < boost::python::len(tile_list); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h: In function ‘void dxtbx::masking::mask_untrusted_circle(scitbx::af::ref >, double, double, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:79:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 79 | for (std::size_t j = y0; j < y1; ++j) { - | ~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:80:34: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 80 | for (std::size_t i = x0; i < x1; ++i) { - | ~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h: In function ‘void dxtbx::masking::mask_untrusted_polygon(scitbx::af::ref >, const scitbx::af::const_ref >&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:143:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 143 | for (std::size_t j = y0; j < y1; ++j) { - | ~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:144:34: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 144 | for (std::size_t i = x0; i < x1; ++i) { - | ~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘static void dxtbx::format::boost_python::ImagePickleSuite::setstate(dxtbx::format::Image&, boost::python::tuple) [with T = double]’: -/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ - 345 | &PickleSuiteType::setstate, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:134:18: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = double]’ - 122 | class_(name) - | ~~~~~~~~~~~~~~~~~~~~~~~~ - 123 | .def(init()) - | ~~~~~~~~~~~~~~~~~~~~~~~ - 124 | .def("__init__", make_constructor(&make_image_from_flex)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 125 | .def("__init__", make_constructor(&make_image_from_tuple)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 126 | .def("__getitem__", &image_type::tile) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 127 | .def("tile", &image_type::tile) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 128 | .def("tile_names", &image_type::tile_names) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 129 | .def("n_tiles", &image_type::n_tiles) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 130 | .def("empty", &image_type::empty) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 131 | .def("append", &image_type::push_back) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 132 | .def("__len__", &image_type::n_tiles) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 133 | .def("__iter__", range(&image_type::begin, &image_type::end)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 134 | .def_pickle(ImagePickleSuite()); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:143:26: required from here - 143 | image_wrapper("ImageDouble"); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:98:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 98 | for (std::size_t i = 0; i < boost::python::len(tile_list); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = unsigned char; grid = scitbx::af::versa >]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: recursively required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ - 249 | return get_buffer(ptr); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here - 254 | return get_buffer(obj.ptr()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:24, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:9: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: @@ -10558,20 +10308,6 @@ 408 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:409:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 409 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = short unsigned int; grid = scitbx::af::versa >]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: recursively required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ - 249 | return get_buffer(ptr); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here - 254 | return get_buffer(obj.ptr()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:449:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; @@ -10590,20 +10326,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 89 | for (std::size_t i = 0; i < n_angles; ++i) { | ~~^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = unsigned int; grid = scitbx::af::versa >]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: recursively required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ - 249 | return get_buffer(ptr); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here - 254 | return get_buffer(obj.ptr()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { - | ~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, @@ -10643,6 +10365,84 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:7: note: in expansion of macro ‘DXTBX_ASSERT’ 417 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = bool; grid = scitbx::af::versa >]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:247:31: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ + 247 | return get_buffer_specific(obj); + | ~~~~~~~~~~~~~~~~~~~^~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here + 254 | return get_buffer(obj.ptr()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = long unsigned int; grid = scitbx::af::versa >]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:247:31: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ + 247 | return get_buffer_specific(obj); + | ~~~~~~~~~~~~~~~~~~~^~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ + 249 | return get_buffer(ptr); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here + 254 | return get_buffer(obj.ptr()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = unsigned char; grid = scitbx::af::versa >]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: recursively required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ + 249 | return get_buffer(ptr); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here + 254 | return get_buffer(obj.ptr()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = short unsigned int; grid = scitbx::af::versa >]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: recursively required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ + 249 | return get_buffer(ptr); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here + 254 | return get_buffer(obj.ptr()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = unsigned int; grid = scitbx::af::versa >]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: recursively required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ + 249 | return get_buffer(ptr); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:254:36: required from here + 254 | return get_buffer(obj.ptr()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:64:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 64 | for (int i = 0; i < flex.accessor().nd(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { + | ~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = int; grid = scitbx::af::versa >]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: recursively required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ 249 | return get_buffer(ptr); @@ -10713,15 +10513,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:66:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 66 | for (int j = i + 1; j < flex.accessor().nd(); ++j) { | ~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/detector.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ^~~~~~~~~~~~ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc: In instantiation of ‘pybind11::buffer_info get_buffer_specific(grid) [with T = double; grid = scitbx::af::versa >]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:249:32: recursively required from ‘pybind11::buffer_info get_buffer(PyObject*) [with T = scitbx::af::versa >; Q = scitbx::af::versa >; Args = {scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >, scitbx::af::versa, scitbx::af::flex_grid > >}; PyObject = _object]’ 249 | return get_buffer(ptr); @@ -10834,13 +10625,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/flumpy.cc:115:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 115 | for (int j = i + 1; j < dim_sizes.size(); ++j) { | ~~^~~~~~~~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/experiment.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o dxtbx/src/dxtbx/model/boost_python/experiment_list.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o dxtbx/src/dxtbx/model/boost_python/goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:17: +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/boost_python/ext.cc:3: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] 562 | double wavelength_; @@ -10899,9 +10685,7 @@ 760 | return scitbx::af::shared >(1, (0., 0., 0.)); | ^~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:18: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:17: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:288:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; @@ -10929,12 +10713,163 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 436 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 89 | for (std::size_t i = 0; i < n_angles; ++i) { - | ~~^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h: In function ‘void dxtbx::masking::mask_untrusted_circle(scitbx::af::ref >, double, double, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:79:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 79 | for (std::size_t j = y0; j < y1; ++j) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:80:34: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 80 | for (std::size_t i = x0; i < x1; ++i) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h: In function ‘void dxtbx::masking::mask_untrusted_polygon(scitbx::af::ref >, const scitbx::af::const_ref >&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:143:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 143 | for (std::size_t j = y0; j < y1; ++j) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:144:34: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 144 | for (std::size_t i = x0; i < x1; ++i) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘std::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = bool]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:125:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = bool]’ + 125 | .def("__init__", make_constructor(&make_image_from_tuple)) + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:141:24: required from here + 141 | image_wrapper("ImageBool"); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:51:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 51 | for (std::size_t i = 0; i < boost::python::len(data); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘std::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:125:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = int]’ + 125 | .def("__init__", make_constructor(&make_image_from_tuple)) + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:142:23: required from here + 142 | image_wrapper("ImageInt"); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:51:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 51 | for (std::size_t i = 0; i < boost::python::len(data); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘std::shared_ptr > dxtbx::format::boost_python::make_image_from_tuple(boost::python::tuple) [with T = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:125:40: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = double]’ + 125 | .def("__init__", make_constructor(&make_image_from_tuple)) + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:143:26: required from here + 143 | image_wrapper("ImageDouble"); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:51:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 51 | for (std::size_t i = 0; i < boost::python::len(data); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘static void dxtbx::format::boost_python::ImagePickleSuite::setstate(dxtbx::format::Image&, boost::python::tuple) [with T = bool]’: +/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ + 345 | &PickleSuiteType::setstate, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:134:18: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = bool]’ + 122 | class_(name) + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 123 | .def(init()) + | ~~~~~~~~~~~~~~~~~~~~~~~ + 124 | .def("__init__", make_constructor(&make_image_from_flex)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 125 | .def("__init__", make_constructor(&make_image_from_tuple)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 126 | .def("__getitem__", &image_type::tile) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 127 | .def("tile", &image_type::tile) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 128 | .def("tile_names", &image_type::tile_names) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 129 | .def("n_tiles", &image_type::n_tiles) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 130 | .def("empty", &image_type::empty) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 131 | .def("append", &image_type::push_back) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 132 | .def("__len__", &image_type::n_tiles) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 133 | .def("__iter__", range(&image_type::begin, &image_type::end)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 134 | .def_pickle(ImagePickleSuite()); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:141:24: required from here + 141 | image_wrapper("ImageBool"); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:98:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 98 | for (std::size_t i = 0; i < boost::python::len(tile_list); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘static void dxtbx::format::boost_python::ImagePickleSuite::setstate(dxtbx::format::Image&, boost::python::tuple) [with T = int]’: +/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ + 345 | &PickleSuiteType::setstate, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:134:18: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = int]’ + 122 | class_(name) + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 123 | .def(init()) + | ~~~~~~~~~~~~~~~~~~~~~~~ + 124 | .def("__init__", make_constructor(&make_image_from_flex)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 125 | .def("__init__", make_constructor(&make_image_from_tuple)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 126 | .def("__getitem__", &image_type::tile) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 127 | .def("tile", &image_type::tile) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 128 | .def("tile_names", &image_type::tile_names) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 129 | .def("n_tiles", &image_type::n_tiles) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 130 | .def("empty", &image_type::empty) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 131 | .def("append", &image_type::push_back) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 132 | .def("__len__", &image_type::n_tiles) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 133 | .def("__iter__", range(&image_type::begin, &image_type::end)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 134 | .def_pickle(ImagePickleSuite()); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:142:23: required from here + 142 | image_wrapper("ImageInt"); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:98:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 98 | for (std::size_t i = 0; i < boost::python::len(tile_list); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc: In instantiation of ‘static void dxtbx::format::boost_python::ImagePickleSuite::setstate(dxtbx::format::Image&, boost::python::tuple) [with T = double]’: +/usr/include/boost/python/class.hpp:345:9: required from ‘boost::python::class_::self& boost::python::class_::def_pickle(const PickleSuiteType&) [with PickleSuiteType = dxtbx::format::boost_python::ImagePickleSuite; W = dxtbx::format::Image; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’ + 345 | &PickleSuiteType::setstate, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:134:18: required from ‘void dxtbx::format::boost_python::image_wrapper(const char*) [with T = double]’ + 122 | class_(name) + | ~~~~~~~~~~~~~~~~~~~~~~~~ + 123 | .def(init()) + | ~~~~~~~~~~~~~~~~~~~~~~~ + 124 | .def("__init__", make_constructor(&make_image_from_flex)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 125 | .def("__init__", make_constructor(&make_image_from_tuple)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 126 | .def("__getitem__", &image_type::tile) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 127 | .def("tile", &image_type::tile) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 128 | .def("tile_names", &image_type::tile_names) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 129 | .def("n_tiles", &image_type::n_tiles) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 130 | .def("empty", &image_type::empty) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 131 | .def("append", &image_type::push_back) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 132 | .def("__len__", &image_type::n_tiles) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 133 | .def("__iter__", range(&image_type::begin, &image_type::end)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 134 | .def_pickle(ImagePickleSuite()); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:143:26: required from here + 143 | image_wrapper("ImageDouble"); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/format/boost_python/image_ext.cc:98:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 98 | for (std::size_t i = 0; i < boost::python::len(tile_list); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o dxtbx/src/dxtbx/model/boost_python/detector.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/goniometer_shadow_masking.h:12, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:30: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h: In function ‘void dxtbx::masking::mask_untrusted_circle(scitbx::af::ref >, double, double, double)’: @@ -10951,57 +10886,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/masking/masking.h:144:34: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 144 | for (std::size_t i = x0; i < x1; ++i) { | ~~^~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/vec3.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:17: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >&, int)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:44: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 148 | DXTBX_ASSERT(properties_table.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 148 | DXTBX_ASSERT(properties_table.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_properties(dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:37: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 242 | DXTBX_ASSERT(new_table.size() == num_images_); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 242 | DXTBX_ASSERT(new_table.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_oscillation(scitbx::vec2)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:397:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 397 | for (std::size_t i = 0; i < num_images_; ++i) { - | ~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_exposure_times(scitbx::af::shared)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:42: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_epochs(const scitbx::af::shared&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:34: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 417 | DXTBX_ASSERT(epochs.size() == num_images_); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 417 | DXTBX_ASSERT(epochs.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ^~~~~~~~~~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.cc /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h: In member function ‘dxtbx::format::ImageBuffer dxtbx::ImageSet::get_raw_data(std::size_t)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:648:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 648 | if (data_cache_.index == index) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h: In member function ‘dxtbx::format::Image dxtbx::ImageSet::get_raw_data_as_double(std::size_t)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:1116:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1116 | if (double_raw_data_cache_.index == index) { @@ -11050,22 +10938,95 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:1415:5: note: in expansion of macro ‘DXTBX_ASSERT’ 1415 | DXTBX_ASSERT(scan->get_num_images() == size()); | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In function ‘void dxtbx::model::boost_python::beam_detail::Beam_set_s0_at_scan_points_from_tuple(dxtbx::model::Beam&, boost::python::tuple)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:209:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 209 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In function ‘void dxtbx::model::boost_python::beam_detail::Beam_set_s0_at_scan_points_from_list(dxtbx::model::Beam&, boost::python::list)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:219:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 219 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In static member function ‘static boost::python::tuple dxtbx::model::boost_python::PolychromaticBeamPickleSuite::getstate(boost::python::api::object)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:302:32: warning: unused variable ‘beam’ [-Wunused-variable] - 302 | const PolychromaticBeam &beam = - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In static member function ‘static void dxtbx::model::boost_python::PolychromaticBeamPickleSuite::setstate(boost::python::api::object, boost::python::tuple)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:308:26: warning: unused variable ‘beam’ [-Wunused-variable] - 308 | PolychromaticBeam &beam = boost::python::extract(obj)(); - | ^~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:17: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:551:18: warning: ‘scitbx::vec3 dxtbx::model::Beam::direction_’ [-Wreorder] + 551 | vec3 direction_; + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:93:5: warning: when initialized here [-Wreorder] + 93 | Beam() + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] + 552 | double divergence_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:126:5: warning: when initialized here [-Wreorder] + 126 | Beam(vec3 direction, double wavelength) + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] + 552 | double divergence_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:165:5: warning: when initialized here [-Wreorder] + 165 | Beam(vec3 direction, + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double, scitbx::vec3, double, double, double, dxtbx::model::Probe)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] + 552 | double divergence_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:193:5: warning: when initialized here [-Wreorder] + 193 | Beam(vec3 direction, + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double, scitbx::vec3, double, double, double, dxtbx::model::Probe, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] + 552 | double divergence_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:227:5: warning: when initialized here [-Wreorder] + 227 | Beam(vec3 direction, + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In member function ‘virtual scitbx::af::shared > dxtbx::model::PolychromaticBeam::get_s0_at_scan_points() const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:52: warning: left operand of comma operator has no effect [-Wunused-value] + 760 | return scitbx::af::shared >(1, (0., 0., 0.)); + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] + 760 | return scitbx::af::shared >(1, (0., 0., 0.)); + | ^~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:18: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:288:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:289:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 289 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:328:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 328 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:329:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 329 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:408:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 408 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:409:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 409 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:449:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h: In member function ‘void dxtbx::model::Panel::apply_untrusted_rectangle_mask(scitbx::af::ref >) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:435:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 435 | for (std::size_t y = y0; y < y1; ++y) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 436 | for (std::size_t x = x0; x < x1; ++x) { + | ~~^~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h: In instantiation of ‘dxtbx::format::Image dxtbx::ImageSetData::get_image_from_tuple(boost::python::tuple) [with T = double]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:469:56: required from here 469 | buffer = ImageBuffer(get_image_from_tuple(obj)); @@ -11073,6 +11034,12 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:502:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] 502 | for (std::size_t i = 0; i < boost::python::len(obj); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 89 | for (std::size_t i = 0; i < n_angles; ++i) { + | ~~^~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h: In instantiation of ‘dxtbx::format::Image dxtbx::ImageSetData::get_image_from_tuple(boost::python::tuple) [with T = float]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:471:55: required from here 471 | buffer = ImageBuffer(get_image_from_tuple(obj)); @@ -11087,6 +11054,18 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/imageset.h:502:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] 502 | for (std::size_t i = 0; i < boost::python::len(obj); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc: In function ‘void dxtbx::model::boost_python::Crystal_set_A_at_scan_points_from_tuple(dxtbx::model::CrystalBase&, boost::python::tuple)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:119:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 119 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc: In function ‘void dxtbx::model::boost_python::Crystal_set_A_at_scan_points_from_list(dxtbx::model::CrystalBase&, boost::python::list)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:129:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 129 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc: In function ‘void dxtbx::model::boost_python::Crystal_set_B_covariance_from_tuple(dxtbx::model::CrystalBase&, boost::python::api::object)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:141:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 141 | for (std::size_t i = 0; i < boost::python::len(obj); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc: In instantiation of ‘static void dxtbx::boost_python::ImageSetDataPickleSuite::set_model_list(dxtbx::ImageSetData&, boost::python::tuple, Func) [with Model = dxtbx::model::BeamBase; Func = void (dxtbx::ImageSetData::*)(const std::shared_ptr&, long unsigned int)]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:249:56: required from here 249 | ImageSetDataPickleSuite::set_model_list( @@ -11151,18 +11130,77 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/boost_python/imageset_ext.cc:235:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] 235 | for (std::size_t i = 0; i < boost::python::len(indices); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc: In function ‘void dxtbx::model::boost_python::Crystal_set_A_at_scan_points_from_tuple(dxtbx::model::CrystalBase&, boost::python::tuple)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:119:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 119 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc: In function ‘void dxtbx::model::boost_python::Crystal_set_A_at_scan_points_from_list(dxtbx::model::CrystalBase&, boost::python::list)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:129:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 129 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc: In function ‘void dxtbx::model::boost_python::Crystal_set_B_covariance_from_tuple(dxtbx::model::CrystalBase&, boost::python::api::object)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/crystal.cc:141:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 141 | for (std::size_t i = 0; i < boost::python::len(obj); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o dxtbx/src/dxtbx/model/boost_python/experiment.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o dxtbx/src/dxtbx/model/boost_python/experiment_list.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/vec3.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:17: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >&, int)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:44: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 148 | DXTBX_ASSERT(properties_table.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 148 | DXTBX_ASSERT(properties_table.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_properties(dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:37: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 242 | DXTBX_ASSERT(new_table.size() == num_images_); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 242 | DXTBX_ASSERT(new_table.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_oscillation(scitbx::vec2)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:397:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 397 | for (std::size_t i = 0; i < num_images_; ++i) { + | ~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_exposure_times(scitbx::af::shared)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:42: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_epochs(const scitbx::af::shared&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:34: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 417 | DXTBX_ASSERT(epochs.size() == num_images_); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 417 | DXTBX_ASSERT(epochs.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ^~~~~~~~~~~~ +g++ -o dxtbx/src/dxtbx/model/boost_python/goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In function ‘void dxtbx::model::boost_python::beam_detail::Beam_set_s0_at_scan_points_from_tuple(dxtbx::model::Beam&, boost::python::tuple)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:209:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 209 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In function ‘void dxtbx::model::boost_python::beam_detail::Beam_set_s0_at_scan_points_from_list(dxtbx::model::Beam&, boost::python::list)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:219:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 219 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In static member function ‘static boost::python::tuple dxtbx::model::boost_python::PolychromaticBeamPickleSuite::getstate(boost::python::api::object)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:302:32: warning: unused variable ‘beam’ [-Wunused-variable] + 302 | const PolychromaticBeam &beam = + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc: In static member function ‘static void dxtbx::model::boost_python::PolychromaticBeamPickleSuite::setstate(boost::python::api::object, boost::python::tuple)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/beam.cc:308:26: warning: unused variable ‘beam’ [-Wunused-variable] + 308 | PolychromaticBeam &beam = boost::python::extract(obj)(); + | ^~~~ +g++ -o dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o dxtbx/src/dxtbx/model/boost_python/model_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/model_ext.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/virtual_panel.h:28, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel_data.h:17, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:16, @@ -11297,6 +11335,13 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:7: note: in expansion of macro ‘DXTBX_ASSERT’ 417 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ^~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment.h:22, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment.cc:17: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: @@ -11356,13 +11401,40 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] 760 | return scitbx::af::shared >(1, (0., 0., 0.)); | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘void dxtbx::model::boost_python::detector_detail::node_from_dict(boost::python::dict, dxtbx::model::Detector::Node*, boost::python::list, scitbx::af::ref)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:88:34: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 88 | DXTBX_ASSERT(used.size() == boost::python::len(panels)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:88:9: note: in expansion of macro ‘DXTBX_ASSERT’ + 88 | DXTBX_ASSERT(used.size() == boost::python::len(panels)); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:89:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 89 | DXTBX_ASSERT(idx < boost::python::len(panels)); + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:89:9: note: in expansion of macro ‘DXTBX_ASSERT’ + 89 | DXTBX_ASSERT(idx < boost::python::len(panels)); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:100:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 100 | for (std::size_t i = 0; i < boost::python::len(obj["children"]); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘dxtbx::model::Detector* dxtbx::model::boost_python::detector_detail::detector_from_dict(dxtbx::model::Detector*, boost::python::dict)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:124:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 124 | for (std::size_t i = 0; i < boost::python::len(hierarchy["children"]); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:134:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 134 | for (std::size_t i = 0; i < boost::python::len(panels); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘dxtbx::model::Detector* dxtbx::model::boost_python::detector_detail::detector_from_dict(dxtbx::model::Detector*, boost::python::dict, const dxtbx::format::Image&, const dxtbx::format::Image&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:158:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 158 | for (std::size_t i = 0; i < boost::python::len(hierarchy["children"]); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:168:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 168 | for (std::size_t i = 0; i < boost::python::len(panels); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In static member function ‘static void dxtbx::model::boost_python::detector_detail::DetectorPickleSuite::copy_node(dxtbx::model::Detector::Node::pointer, boost::python::dict, boost::python::list)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:228:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 228 | for (std::size_t i = 0; i < boost::python::len(node["children"]); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment.h:23: @@ -11393,6 +11465,12 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 436 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment.h:25: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 89 | for (std::size_t i = 0; i < n_angles; ++i) { + | ~~^~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment.h:22, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment_list.h:23, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:20: @@ -11446,12 +11524,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:227:5: warning: when initialized here [-Wreorder] 227 | Beam(vec3 direction, | ^~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment.h:25: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 89 | for (std::size_t i = 0; i < n_angles; ++i) { - | ~~^~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In member function ‘virtual scitbx::af::shared > dxtbx::model::PolychromaticBeam::get_s0_at_scan_points() const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:52: warning: left operand of comma operator has no effect [-Wunused-value] 760 | return scitbx::af::shared >(1, (0., 0., 0.)); @@ -11459,40 +11531,65 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] 760 | return scitbx::af::shared >(1, (0., 0., 0.)); | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘void dxtbx::model::boost_python::detector_detail::node_from_dict(boost::python::dict, dxtbx::model::Detector::Node*, boost::python::list, scitbx::af::ref)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:88:34: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 88 | DXTBX_ASSERT(used.size() == boost::python::len(panels)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:88:9: note: in expansion of macro ‘DXTBX_ASSERT’ - 88 | DXTBX_ASSERT(used.size() == boost::python::len(panels)); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:89:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 89 | DXTBX_ASSERT(idx < boost::python::len(panels)); - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:89:9: note: in expansion of macro ‘DXTBX_ASSERT’ - 89 | DXTBX_ASSERT(idx < boost::python::len(panels)); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:100:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 100 | for (std::size_t i = 0; i < boost::python::len(obj["children"]); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘dxtbx::model::Detector* dxtbx::model::boost_python::detector_detail::detector_from_dict(dxtbx::model::Detector*, boost::python::dict)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:124:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 124 | for (std::size_t i = 0; i < boost::python::len(hierarchy["children"]); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:134:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 134 | for (std::size_t i = 0; i < boost::python::len(panels); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In function ‘dxtbx::model::Detector* dxtbx::model::boost_python::detector_detail::detector_from_dict(dxtbx::model::Detector*, boost::python::dict, const dxtbx::format::Image&, const dxtbx::format::Image&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:158:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 158 | for (std::size_t i = 0; i < boost::python::len(hierarchy["children"]); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:168:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 168 | for (std::size_t i = 0; i < boost::python::len(panels); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc: In static member function ‘static void dxtbx::model::boost_python::detector_detail::DetectorPickleSuite::copy_node(dxtbx::model::Detector::Node::pointer, boost::python::dict, boost::python::list)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/detector.cc:228:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 228 | for (std::size_t i = 0; i < boost::python::len(node["children"]); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:20: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:551:18: warning: ‘scitbx::vec3 dxtbx::model::Beam::direction_’ [-Wreorder] + 551 | vec3 direction_; + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:93:5: warning: when initialized here [-Wreorder] + 93 | Beam() + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] + 552 | double divergence_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:126:5: warning: when initialized here [-Wreorder] + 126 | Beam(vec3 direction, double wavelength) + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] + 552 | double divergence_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:165:5: warning: when initialized here [-Wreorder] + 165 | Beam(vec3 direction, + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double, scitbx::vec3, double, double, double, dxtbx::model::Probe)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] + 552 | double divergence_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:193:5: warning: when initialized here [-Wreorder] + 193 | Beam(vec3 direction, + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double, scitbx::vec3, double, double, double, dxtbx::model::Probe, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] + 562 | double wavelength_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] + 552 | double divergence_; + | ^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:227:5: warning: when initialized here [-Wreorder] + 227 | Beam(vec3 direction, + | ^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In member function ‘virtual scitbx::af::shared > dxtbx::model::PolychromaticBeam::get_s0_at_scan_points() const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:52: warning: left operand of comma operator has no effect [-Wunused-value] + 760 | return scitbx::af::shared >(1, (0., 0., 0.)); + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] + 760 | return scitbx::af::shared >(1, (0., 0., 0.)); + | ^~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment.h:23: @@ -11514,23 +11611,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:449:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h: In member function ‘void dxtbx::model::Panel::apply_untrusted_rectangle_mask(scitbx::af::ref >) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:435:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 435 | for (std::size_t y = y0; y < y1; ++y) { - | ~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 436 | for (std::size_t x = x0; x < x1; ++x) { - | ~~^~~~ -g++ -o dxtbx/src/dxtbx/model/boost_python/model_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/model_ext.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment.h:25: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 89 | for (std::size_t i = 0; i < n_angles; ++i) { - | ~~^~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, @@ -11544,6 +11624,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:7: note: in expansion of macro ‘DXTBX_ASSERT’ 148 | DXTBX_ASSERT(properties_table.size() == num_images_); | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_properties(dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:37: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 242 | DXTBX_ASSERT(new_table.size() == num_images_); @@ -11551,10 +11633,23 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:7: note: in expansion of macro ‘DXTBX_ASSERT’ 242 | DXTBX_ASSERT(new_table.size() == num_images_); | ^~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:288:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:289:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 289 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:328:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 328 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_oscillation(scitbx::vec2)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:397:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 397 | for (std::size_t i = 0; i < num_images_; ++i) { | ~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:329:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 329 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_exposure_times(scitbx::af::shared)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:42: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); @@ -11569,6 +11664,49 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:7: note: in expansion of macro ‘DXTBX_ASSERT’ 417 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:408:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 408 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:409:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 409 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:449:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h: In member function ‘void dxtbx::model::Panel::apply_untrusted_rectangle_mask(scitbx::af::ref >) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:435:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 435 | for (std::size_t y = y0; y < y1; ++y) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 436 | for (std::size_t x = x0; x < x1; ++x) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h: In member function ‘void dxtbx::model::Panel::apply_untrusted_rectangle_mask(scitbx::af::ref >) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:435:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 435 | for (std::size_t y = y0; y < y1; ++y) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 436 | for (std::size_t x = x0; x < x1; ++x) { + | ~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ^~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 89 | for (std::size_t i = 0; i < n_angles; ++i) { + | ~~^~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/experiment.h:25: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 89 | for (std::size_t i = 0; i < n_angles; ++i) { + | ~~^~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, @@ -11607,135 +11745,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:7: note: in expansion of macro ‘DXTBX_ASSERT’ 417 | DXTBX_ASSERT(epochs.size() == num_images_); | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘dxtbx::model::ExperimentList* dxtbx::model::boost_python::make_experiment_list(boost::python::api::object)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:30:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 30 | for (std::size_t i = 0; i < boost::python::len(items); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘void dxtbx::model::boost_python::experiment_list_setitem(dxtbx::model::ExperimentList&, int, dxtbx::model::Experiment)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:174:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 174 | if (n >= self.size() || n < 0) { - | ~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘dxtbx::model::Experiment& dxtbx::model::boost_python::experiment_list_getitem(dxtbx::model::ExperimentList&, int)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:184:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 184 | if (n >= self.size() || n < 0) { - | ~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘dxtbx::model::ExperimentList dxtbx::model::boost_python::experiment_list_getitem_slice(const dxtbx::model::ExperimentList&, boost::python::slice)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:193:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] - 193 | for (std::size_t i = as.start; i < as.stop && i < self.size(); i += as.step) { - | ~~^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘void dxtbx::model::boost_python::experiment_list_delitem(dxtbx::model::ExperimentList&, int)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:203:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 203 | if (n >= self.size() || n < 0) { - | ~~^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:20: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:551:18: warning: ‘scitbx::vec3 dxtbx::model::Beam::direction_’ [-Wreorder] - 551 | vec3 direction_; - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:93:5: warning: when initialized here [-Wreorder] - 93 | Beam() - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] - 552 | double divergence_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:126:5: warning: when initialized here [-Wreorder] - 126 | Beam(vec3 direction, double wavelength) - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] - 552 | double divergence_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:165:5: warning: when initialized here [-Wreorder] - 165 | Beam(vec3 direction, - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double, scitbx::vec3, double, double, double, dxtbx::model::Probe)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] - 552 | double divergence_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:193:5: warning: when initialized here [-Wreorder] - 193 | Beam(vec3 direction, - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam(scitbx::vec3, double, double, double, scitbx::vec3, double, double, double, dxtbx::model::Probe, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] - 562 | double wavelength_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:552:12: warning: ‘double dxtbx::model::Beam::divergence_’ [-Wreorder] - 552 | double divergence_; - | ^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:227:5: warning: when initialized here [-Wreorder] - 227 | Beam(vec3 direction, - | ^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In member function ‘virtual scitbx::af::shared > dxtbx::model::PolychromaticBeam::get_s0_at_scan_points() const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:52: warning: left operand of comma operator has no effect [-Wunused-value] - 760 | return scitbx::af::shared >(1, (0., 0., 0.)); - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] - 760 | return scitbx::af::shared >(1, (0., 0., 0.)); - | ^~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:288:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:289:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 289 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:328:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 328 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:329:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 329 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:408:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 408 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:409:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 409 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:449:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h: In member function ‘void dxtbx::model::Panel::apply_untrusted_rectangle_mask(scitbx::af::ref >) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:435:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 435 | for (std::size_t y = y0; y < y1; ++y) { - | ~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 436 | for (std::size_t x = x0; x < x1; ++x) { - | ~~^~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 89 | for (std::size_t i = 0; i < n_angles; ++i) { - | ~~^~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, @@ -11782,6 +11791,13 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ 556 | DXTBX_ASSERT(properties_.size() == num_images_); | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ^~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc: In function ‘void dxtbx::model::boost_python::goniometer_detail::Goniometer_set_S_at_scan_points_from_tuple(dxtbx::model::Goniometer&, boost::python::tuple)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:79:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] 79 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { @@ -11790,10 +11806,28 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/goniometer.cc:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] 89 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘dxtbx::model::ExperimentList* dxtbx::model::boost_python::make_experiment_list(boost::python::api::object)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:30:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 30 | for (std::size_t i = 0; i < boost::python::len(items); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘void dxtbx::model::boost_python::experiment_list_setitem(dxtbx::model::ExperimentList&, int, dxtbx::model::Experiment)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:174:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 174 | if (n >= self.size() || n < 0) { + | ~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘dxtbx::model::Experiment& dxtbx::model::boost_python::experiment_list_getitem(dxtbx::model::ExperimentList&, int)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:184:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 184 | if (n >= self.size() || n < 0) { + | ~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘dxtbx::model::ExperimentList dxtbx::model::boost_python::experiment_list_getitem_slice(const dxtbx::model::ExperimentList&, boost::python::slice)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:193:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] + 193 | for (std::size_t i = as.start; i < as.stop && i < self.size(); i += as.step) { + | ~~^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc: In function ‘void dxtbx::model::boost_python::experiment_list_delitem(dxtbx::model::ExperimentList&, int)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/experiment_list.cc:203:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 203 | if (n >= self.size() || n < 0) { + | ~~^~~~~~~~~~~~~~ g++ -o dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.cc cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o dxtbx/src/dxtbx/model/boost_python/panel.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/panel.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.cc:18: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: @@ -11939,6 +11973,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.cc:105:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] 105 | for (std::size_t i = 0; i < boost::python::len(l); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -o dxtbx/src/dxtbx/model/boost_python/panel.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/panel.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o dxtbx/src/dxtbx/model/boost_python/parallax_correction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/parallax_correction.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/virtual_panel.h:28, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel_data.h:17, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:16, @@ -12021,8 +12059,6 @@ 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -g++ -o dxtbx/src/dxtbx/model/boost_python/parallax_correction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -isystem/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBUILD_CBF -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -I/usr/include/cbflib -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cbflib_adaptbx -I/usr/include/python3.13 -I/usr/include/hdf5/serial /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/parallax_correction.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h: In member function ‘void dxtbx::model::Panel::apply_untrusted_rectangle_mask(scitbx::af::ref >) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:435:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 435 | for (std::size_t y = y0; y < y1; ++y) { @@ -12106,6 +12142,15 @@ g++ -o exe_dev/cctbx.convert_ccp4_symop_lib -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/convert_ccp4_symop_lib.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm g++ -o exe_dev/cctbx.find_distances -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/find_distances.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm g++ -o exe_dev/cctbx.getting_started -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/getting_started.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm +g++ -o exe_dev/cctbx.lattice_symmetry -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/lattice_symmetry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm +g++ -o exe_dev/cctbx.sym_equiv_sites -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/sym_equiv_sites.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm +g++ -o exe_dev/cctbx.sys_abs_equiv_space_groups -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/sys_abs_equiv_space_groups.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm +g++ -o fable/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o gltbx/font_ucs_10x20.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/font_ucs_10x20.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o gltbx/font_ucs_8x13.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/font_ucs_8x13.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/virtual_panel.h:28, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel_data.h:17, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:16, @@ -12168,7 +12213,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] 760 | return scitbx::af::shared >(1, (0., 0., 0.)); | ^~ -g++ -o exe_dev/cctbx.lattice_symmetry -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/lattice_symmetry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:288:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; @@ -12196,15 +12240,13 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 436 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ -g++ -o exe_dev/cctbx.sym_equiv_sites -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/sym_equiv_sites.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm -g++ -o exe_dev/cctbx.sys_abs_equiv_space_groups -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread cctbx/examples/sys_abs_equiv_space_groups.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lboost_thread -lboost_system -lm -g++ -o fable/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/ext.cpp +g++ -o gltbx/font_ucs_9x15.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/font_ucs_9x15.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o gltbx/font_ucs_10x20.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/font_ucs_10x20.cpp +g++ -o gltbx/fonts_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/gltbx/fonts_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o gltbx/font_ucs_8x13.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/font_ucs_8x13.cpp +g++ -o gltbx/gl_defines_00_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_00_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o gltbx/font_ucs_9x15.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/font_ucs_9x15.cpp +g++ -o gltbx/gl_defines_01_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_01_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:19: @@ -12212,64 +12254,13 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 89 | for (std::size_t i = 0; i < n_angles; ++i) { | ~~^~~~~~~~~~ -g++ -o gltbx/fonts_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/gltbx/fonts_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/scan_helpers.cc:16: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 89 | for (std::size_t i = 0; i < n_angles; ++i) { | ~~^~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/vec2.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:17: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >&, int)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:44: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 148 | DXTBX_ASSERT(properties_table.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 148 | DXTBX_ASSERT(properties_table.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_properties(dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:37: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 242 | DXTBX_ASSERT(new_table.size() == num_images_); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 242 | DXTBX_ASSERT(new_table.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_oscillation(scitbx::vec2)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:397:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 397 | for (std::size_t i = 0; i < num_images_; ++i) { - | ~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_exposure_times(scitbx::af::shared)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:42: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_epochs(const scitbx::af::shared&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:34: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 417 | DXTBX_ASSERT(epochs.size() == num_images_); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 417 | DXTBX_ASSERT(epochs.size() == num_images_); - | ^~~~~~~~~~~~ -g++ -o gltbx/gl_defines_00_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_00_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o gltbx/gl_defines_01_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_01_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ - 556 | DXTBX_ASSERT(properties_.size() == num_images_); - | ^~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:20: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc:10: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] 562 | double wavelength_; @@ -12327,8 +12318,76 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] 760 | return scitbx::af::shared >(1, (0., 0., 0.)); | ^~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/vec2.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:17: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In constructor ‘dxtbx::model::Scan::Scan(scitbx::vec2, dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >&, int)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:44: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 148 | DXTBX_ASSERT(properties_table.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:148:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 148 | DXTBX_ASSERT(properties_table.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_properties(dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:37: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 242 | DXTBX_ASSERT(new_table.size() == num_images_); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:242:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 242 | DXTBX_ASSERT(new_table.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_oscillation(scitbx::vec2)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:397:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 397 | for (std::size_t i = 0; i < num_images_; ++i) { + | ~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_exposure_times(scitbx::af::shared)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:42: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:411:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 411 | DXTBX_ASSERT(exposure_times.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::set_epochs(const scitbx::af::shared&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:34: warning: comparison of integer expressions of different signedness: ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 417 | DXTBX_ASSERT(epochs.size() == num_images_); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:417:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 417 | DXTBX_ASSERT(epochs.size() == num_images_); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h: In member function ‘void dxtbx::model::Scan::append(const dxtbx::model::Scan&, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:39: warning: comparison of integer expressions of different signedness: ‘dxtbx::af::flex_table, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:556:7: note: in expansion of macro ‘DXTBX_ASSERT’ + 556 | DXTBX_ASSERT(properties_.size() == num_images_); + | ^~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:288:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:289:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 289 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:328:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 328 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:329:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 329 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:408:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 408 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:409:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 409 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:449:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] + 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/spectrum.cc:10: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/scan.cc:20: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h: In constructor ‘dxtbx::model::Beam::Beam()’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:562:12: warning: ‘dxtbx::model::Beam::wavelength_’ will be initialized after [-Wreorder] 562 | double wavelength_; @@ -12386,29 +12445,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/beam.h:760:60: warning: right operand of comma operator has no effect [-Wunused-value] 760 | return scitbx::af::shared >(1, (0., 0., 0.)); | ^~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:288:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 288 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:289:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 289 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:328:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 328 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:329:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 329 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_millimeter(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:408:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 408 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:409:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 409 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h: In member function ‘virtual scitbx::vec2 dxtbx::model::OffsetParallaxCorrectedPxMmStrategy::to_pixel(const dxtbx::model::PanelData&, scitbx::vec2) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:449:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 449 | if (i >= dx_.accessor()[1]) i = dx_.accessor()[1] - 1; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/pixel_to_millimeter.h:450:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare] - 450 | if (j >= dx_.accessor()[0]) j = dx_.accessor()[0] - 1; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h: In member function ‘void dxtbx::model::Panel::apply_untrusted_rectangle_mask(scitbx::af::ref >) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:435:36: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 435 | for (std::size_t y = y0; y < y1; ++y) { @@ -12416,6 +12452,12 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 436 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 89 | for (std::size_t i = 0; i < n_angles; ++i) { + | ~~^~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:22, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/detector.h:25, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:18: @@ -12446,12 +12488,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/panel.h:436:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 436 | for (std::size_t x = x0; x < x1; ++x) { | ~~^~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:22, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/boost_python/to_from_dict.h:20: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h: In function ‘scitbx::af::shared dxtbx::model::get_mod2pi_angles_in_range(scitbx::vec2, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan_helpers.h:89:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 89 | for (std::size_t i = 0; i < n_angles; ++i) { - | ~~^~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, @@ -12886,9 +12922,9 @@ g++ -o gltbx/gl_defines_02_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_02_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o gltbx/gl_defines_03_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_03_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o gltbx/gl_defines_04_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_04_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o gltbx/gl_defines_05_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_05_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o gltbx/gl_defines_06_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 gltbx/gl_defines_06_bpl.cpp @@ -12955,8 +12991,6 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/detectors/bruker.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/detectors/bruker.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o iotbx/detectors/bruker_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/detectors/bruker_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/model/scan.h:23: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/array_family/flex_table.h: In member function ‘void dxtbx::af::flex_table::insert_visitor::operator()(T&) const [with T = scitbx::af::shared >; VarientType = boost::variant, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_item, scitbx::af::shared >, boost::mpl::l_end> > > > > > > >]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/array_family/flex_table.h:218:17: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] @@ -12981,6 +13015,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/array_family/flex_table.h:218:50: note: ‘’ declared here 218 | v.insert(v.begin() + pos, n, typename T::value_type()); | ^~~~~~~~~~~~ +g++ -o iotbx/detectors/bruker_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/detectors/bruker_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/array_family/flex_table_suite.h: In function ‘void dxtbx::af::flex_table_suite::type_appender::operator()(U) [with U = scitbx::af::shared >]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/array_family/flex_table_suite.h:905:54: warning: ‘a’ may be used uninitialized [-Wmaybe-uninitialized] 905 | type_list.append(object(handle<>(PyObject_Type(object(a).ptr())))); @@ -13004,8 +13040,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src/dxtbx/array_family/flex_table_suite.h:904:30: note: ‘a’ declared here 904 | typename U::value_type a = typename U::value_type(); | ^ -g++ -o iotbx/detectors/detectors_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/detectors/detectors_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/ccp4_map/ext.cpp: In function ‘void iotbx::ccp4_map::write_ccp4_map_set_grid(const std::string&, const cctbx::uctbx::unit_cell&, const cctbx::sgtbx::space_group&, const scitbx::af::int3&, const scitbx::af::const_ref >&, const scitbx::af::const_ref >&)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/ccp4_map/ext.cpp:178:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 178 | for (int i = 0; i < labels.size(); i++) { @@ -13030,6 +13064,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/ccp4_map/ext.cpp:311:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 311 | for (int i = 0; i < labels.size(); i++) { | ~~^~~~~~~~~~~~~~~ +g++ -o iotbx/detectors/detectors_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/detectors/detectors_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/detectors/image_divider.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/detectors/image_divider.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/dsn6/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/dsn6/ext.cpp @@ -13044,6 +13080,10 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/mtz/column_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/column_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o iotbx/mtz/crystal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o iotbx/mtz/crystal_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -13086,6 +13126,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o iotbx/mtz/dataset.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/dataset.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -13138,8 +13180,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o iotbx/mtz/crystal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -13181,27 +13221,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o iotbx/mtz/crystal_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:30: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] - 591 | IOTBX_ASSERT(iref[0] < oldsize); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ - 591 | IOTBX_ASSERT(iref[0] < oldsize); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:32: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] - 594 | IOTBX_ASSERT(iref[i] < oldsize); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ - 594 | IOTBX_ASSERT(iref[i] < oldsize); - | ^~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -13254,20 +13273,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/column.cpp: In member function ‘void iotbx::mtz::column::set_reals(const scitbx::af::const_ref&, const scitbx::af::const_ref&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/column.cpp:253:48: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 253 | IOTBX_ASSERT(mtz_reflection_indices.size() <= nref_at_entry); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/column.cpp:253:5: note: in expansion of macro ‘IOTBX_ASSERT’ - 253 | IOTBX_ASSERT(mtz_reflection_indices.size() <= nref_at_entry); - | ^~~~~~~~~~~~ -g++ -o iotbx/mtz/dataset.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/dataset.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o iotbx/mtz/dataset_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/dataset_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: @@ -13287,6 +13292,16 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ 594 | IOTBX_ASSERT(iref[i] < oldsize); | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/column.cpp: In member function ‘void iotbx::mtz::column::set_reals(const scitbx::af::const_ref&, const scitbx::af::const_ref&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/column.cpp:253:48: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 253 | IOTBX_ASSERT(mtz_reflection_indices.size() <= nref_at_entry); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/column.cpp:253:5: note: in expansion of macro ‘IOTBX_ASSERT’ + 253 | IOTBX_ASSERT(mtz_reflection_indices.size() <= nref_at_entry); + | ^~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sym_mat3.h:4, @@ -13359,32 +13374,27 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/smart_ptr/shared_array.hpp:23, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/hendrickson_lattman.h:9, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:13: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:30: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] + 591 | IOTBX_ASSERT(iref[0] < oldsize); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ + 591 | IOTBX_ASSERT(iref[0] < oldsize); | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = iotbx::mtz::batch; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ - 130 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 131 | w_t, - | ~~~~ - 132 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 133 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/batch_bpl.cpp:78:60: required from here - 78 | scitbx::af::boost_python::shared_wrapper::wrap( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ - 79 | "shared_batch"); - | ~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:32: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] + 594 | IOTBX_ASSERT(iref[i] < oldsize); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ + 594 | IOTBX_ASSERT(iref[i] < oldsize); + | ^~~~~~~~~~~~ +g++ -o iotbx/mtz/dataset_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/dataset_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -13437,10 +13447,57 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/assert.hpp:58, + from /usr/include/boost/smart_ptr/shared_array.hpp:23, + from /usr/include/boost/shared_array.hpp:17, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/hendrickson_lattman.h:9, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:13: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = iotbx::mtz::batch; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ + 130 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 131 | w_t, + | ~~~~ + 132 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 133 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/batch_bpl.cpp:78:60: required from here + 78 | scitbx::af::boost_python::shared_wrapper::wrap( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ + 79 | "shared_batch"); + | ~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ g++ -o iotbx/mtz/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/mtz/object.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o iotbx/mtz/object_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:30: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] + 591 | IOTBX_ASSERT(iref[0] < oldsize); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ + 591 | IOTBX_ASSERT(iref[0] < oldsize); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:32: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] + 594 | IOTBX_ASSERT(iref[i] < oldsize); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ + 594 | IOTBX_ASSERT(iref[i] < oldsize); + | ^~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sym_mat3.h:4, @@ -13471,10 +13528,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ 594 | IOTBX_ASSERT(iref[i] < oldsize); | ^~~~~~~~~~~~ -g++ -o iotbx/mtz/object_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DMSETS=32 -DMXTALS=32 -DMCOLUMNS=128 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/pdb/atom_selection.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/atom_selection.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o iotbx/pdb/common_residue_names_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/common_residue_names_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_array.hpp:23, from /usr/include/boost/shared_array.hpp:17, @@ -13501,10 +13558,18 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -g++ -o iotbx/pdb/common_residue_names_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/common_residue_names_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sym_mat3.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/rot_mx.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/rt_mx.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/change_of_basis_op.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tr_group.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/space_group.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:12, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/dataset.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal_bpl.cpp:6: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:30: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] 591 | IOTBX_ASSERT(iref[0] < oldsize); @@ -13524,12 +13589,10 @@ | ^~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:31, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/namespace.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/atom_selection.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/hendrickson_lattman.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/sym_equiv.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/asu.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:5: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -13582,12 +13645,42 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/assert.hpp:58, + from /usr/include/boost/smart_ptr/shared_array.hpp:23, + from /usr/include/boost/shared_array.hpp:17, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/hendrickson_lattman.h:9, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:13: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = iotbx::mtz::crystal; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ + 130 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 131 | w_t, + | ~~~~ + 132 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 133 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal_bpl.cpp:42:60: required from here + 42 | scitbx::af::boost_python::shared_wrapper::wrap( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ + 43 | "shared_crystal"); + | ~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +g++ -o iotbx/pdb/construct_hierarchy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/construct_hierarchy.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/hendrickson_lattman.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/sym_equiv.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/miller/asu.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:5: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:31, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/namespace.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/atom_selection.cpp:1: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -13640,63 +13733,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o iotbx/pdb/construct_hierarchy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/construct_hierarchy.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sym_mat3.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/rot_mx.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/rt_mx.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/change_of_basis_op.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tr_group.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/space_group.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:12, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/dataset.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal_bpl.cpp:6: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:30: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] - 591 | IOTBX_ASSERT(iref[0] < oldsize); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ - 591 | IOTBX_ASSERT(iref[0] < oldsize); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:32: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] - 594 | IOTBX_ASSERT(iref[i] < oldsize); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ - 594 | IOTBX_ASSERT(iref[i] < oldsize); - | ^~~~~~~~~~~~ -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/smart_ptr/shared_array.hpp:23, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/hendrickson_lattman.h:9, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:13: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_wrapper.h:130:52: required from ‘static boost::python::class_ > scitbx::af::boost_python::shared_wrapper::wrap(const std::string&) [with ElementType = iotbx::mtz::crystal; GetitemReturnValuePolicy = boost::python::return_value_policy; std::string = std::__cxx11::basic_string]’ - 130 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 131 | w_t, - | ~~~~ - 132 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 133 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/crystal_bpl.cpp:42:60: required from here - 42 | scitbx::af::boost_python::shared_wrapper::wrap( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ - 43 | "shared_crystal"); - | ~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -13723,6 +13759,25 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:30: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] + 591 | IOTBX_ASSERT(iref[0] < oldsize); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ + 591 | IOTBX_ASSERT(iref[0] < oldsize); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:32: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] + 594 | IOTBX_ASSERT(iref[i] < oldsize); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ + 594 | IOTBX_ASSERT(iref[i] < oldsize); + | ^~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -13758,25 +13813,27 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h: In member function ‘void iotbx::mtz::object::delete_reflections(const scitbx::af::const_ref&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:30: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] - 591 | IOTBX_ASSERT(iref[0] < oldsize); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:591:9: note: in expansion of macro ‘IOTBX_ASSERT’ - 591 | IOTBX_ASSERT(iref[0] < oldsize); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:32: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare] - 594 | IOTBX_ASSERT(iref[i] < oldsize); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp: In member function ‘void iotbx::mtz::object::replace_miller_indices(const scitbx::af::const_ref >&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:433:40: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 433 | IOTBX_ASSERT(miller_indices.size() == n_reflections()); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.h:594:11: note: in expansion of macro ‘IOTBX_ASSERT’ - 594 | IOTBX_ASSERT(iref[i] < oldsize); - | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:433:5: note: in expansion of macro ‘IOTBX_ASSERT’ + 433 | IOTBX_ASSERT(miller_indices.size() == n_reflections()); + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:435:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 435 | for(int i_refl=0;i_refl iotbx::mtz::object::extract_integers(const scitbx::af::const_ref&, const char*) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:624:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 624 | for(int i=0;i iotbx::mtz::object::extract_reals(const scitbx::af::const_ref&, const char*) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:684:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 684 | for(int i=0;i::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -13803,27 +13860,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp: In member function ‘void iotbx::mtz::object::replace_miller_indices(const scitbx::af::const_ref >&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:433:40: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 433 | IOTBX_ASSERT(miller_indices.size() == n_reflections()); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:433:5: note: in expansion of macro ‘IOTBX_ASSERT’ - 433 | IOTBX_ASSERT(miller_indices.size() == n_reflections()); - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:435:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 435 | for(int i_refl=0;i_refl iotbx::mtz::object::extract_integers(const scitbx::af::const_ref&, const char*) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:624:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 624 | for(int i=0;i iotbx::mtz::object::extract_reals(const scitbx::af::const_ref&, const char*) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/mtz/object.cpp:684:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 684 | for(int i=0;i class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] @@ -14086,6 +14120,8 @@ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ +g++ -o iotbx/pdb/hierarchy_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/pdb/hierarchy_select.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_select.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/pdb/hierarchy_write.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_write.cpp @@ -14150,6 +14186,9 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o iotbx/pdb/hybrid_36_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hybrid_36_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +gcc -o iotbx/pdb/hybrid_36_c.o -c -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hybrid_36_c.c In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -14185,8 +14224,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o iotbx/pdb/hybrid_36_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hybrid_36_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -14213,7 +14250,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -o iotbx/pdb/hybrid_36_c.o -c -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hybrid_36_c.c +g++ -o iotbx/pdb/hybrid_36_cpp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hybrid_36_cpp.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms.h: At global scope: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms.h:157:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 157 | std::auto_ptr @@ -14230,9 +14268,9 @@ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ -g++ -o iotbx/pdb/hybrid_36_cpp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hybrid_36_cpp.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/pdb/hybrid_36_fem.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable iotbx/pdb/hybrid_36_fem.cpp +g++ -o iotbx/pdb/input.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:2: @@ -14240,34 +14278,21 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 157 | std::auto_ptr - | ^~~~~~~~ -In file included from /usr/include/c++/15/memory:80, - from /usr/include/boost/config/no_tr1/memory.hpp:21, - from /usr/include/boost/get_pointer.hpp:14, - from /usr/include/boost/python/object/pointer_holder.hpp:11, - from /usr/include/boost/python/to_python_indirect.hpp:10, - from /usr/include/boost/python/converter/arg_to_python.hpp:10, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object/class.hpp:9, - from /usr/include/boost/python/class.hpp:13, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_ext.cpp:4: -/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here - 58 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms.h:163:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 163 | std::auto_ptr - | ^~~~~~~~ -/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here - 58 | template class auto_ptr; - | ^~~~~~~~ -g++ -o iotbx/pdb/input.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/pdb/input_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o iotbx/pdb/input_write.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input_write.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/io.hpp:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/close_chain.hpp:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/common.hpp:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/read.hpp:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/major_types.hpp:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem.hpp:10, + from iotbx/pdb/hybrid_36_fem.cpp:1: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/simple_streams.hpp: In member function ‘virtual void fem::utils::simple_ostream_to_char_ptr_and_size::put(char)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/simple_streams.hpp:63:13: warning: comparison of integer expressions of different signedness: ‘fem::ssize_t’ {aka ‘long int’} and ‘fem::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 63 | if (i < sz) s[i++] = c; + | ~~^~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:13: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms.h: At global scope: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms.h:157:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] @@ -14291,24 +14316,6 @@ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp: In function ‘void iotbx::pdb::hierarchy::atoms::bpl_wrap()’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:84:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 84 | std::auto_ptr, - | ^~~~~~~~ -/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here - 58 | template class auto_ptr; - | ^~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/io.hpp:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/close_chain.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/common.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/read.hpp:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/major_types.hpp:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem.hpp:10, - from iotbx/pdb/hybrid_36_fem.cpp:1: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/simple_streams.hpp: In member function ‘virtual void fem::utils::simple_ostream_to_char_ptr_and_size::put(char)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/simple_streams.hpp:63:13: warning: comparison of integer expressions of different signedness: ‘fem::ssize_t’ {aka ‘long int’} and ‘fem::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 63 | if (i < sz) s[i++] = c; - | ~~^~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/common.hpp: In member function ‘void fem::common::getarg(int, fem::str_ref) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/common.hpp:40:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 40 | if (pos < 0 || pos >= command_line_args.buffer.size()) { @@ -14323,12 +14330,111 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/read.hpp:653:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 653 | if (iw+1 != ed.size()) { | ~~~~~^~~~~~~~~~~~ +g++ -o iotbx/pdb/overall_counts.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/overall_counts.cpp In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/variant.hpp:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/major_types.hpp:7: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/equivalence.hpp: In member function ‘void fem::utils::equivalence::array_alignment::infer_diffs0_from_diff_matrix()’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/equivalence.hpp:93:28: warning: comparison of integer expressions of different signedness: ‘const fem::ssize_t’ {aka ‘const long int’} and ‘fem::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 93 | if (c0e[0] == i0) { | ~~~~~~~^~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp: In function ‘void iotbx::pdb::hierarchy::atoms::bpl_wrap()’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms_bpl.cpp:84:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 84 | std::auto_ptr, + | ^~~~~~~~ +/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here + 58 | template class auto_ptr; + | ^~~~~~~~ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:31, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/namespace.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input.cpp:1: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/major_types.hpp:8: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/write.hpp: In destructor ‘fem::write_loop::~write_loop()’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/write.hpp:704:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 704 | while (pos < internal_file_len) { + | ~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_ext.cpp:11: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms.h:157:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 157 | std::auto_ptr + | ^~~~~~~~ +In file included from /usr/include/c++/15/memory:80, + from /usr/include/boost/config/no_tr1/memory.hpp:21, + from /usr/include/boost/get_pointer.hpp:14, + from /usr/include/boost/python/object/pointer_holder.hpp:11, + from /usr/include/boost/python/to_python_indirect.hpp:10, + from /usr/include/boost/python/converter/arg_to_python.hpp:10, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/object/class.hpp:9, + from /usr/include/boost/python/class.hpp:13, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_ext.cpp:4: +/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here + 58 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy_atoms.h:163:8: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 163 | std::auto_ptr + | ^~~~~~~~ +/usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here + 58 | template class auto_ptr; + | ^~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:6: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -14340,11 +14446,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/major_types.hpp:8: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/write.hpp: In destructor ‘fem::write_loop::~write_loop()’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/write.hpp:704:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 704 | while (pos < internal_file_len) { - | ~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); @@ -14355,8 +14456,24 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ -g++ -o iotbx/pdb/input_write.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input_write.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/file_utils.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input.cpp:3: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h: In function ‘scitbx::af::shared > scitbx::misc::split_lines(const char*, std::size_t, bool, bool)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:24:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 24 | while (i < size) { + | ~~^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:25:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 25 | while (i < size && data[i] != '\n' && data[i] != '\r') i++; + | ~~^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:27:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 27 | if (i < size) { + | ~~^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:28:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 28 | if (data[i] == '\r' && i+1 < size && data[i+1] == '\n') { + | ~~~~^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:46:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 46 | if (j < size) { + | ~~^~~~~~ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/function/function_base.hpp:28, from /usr/include/boost/function/detail/prologue.hpp:18, @@ -14417,8 +14534,7 @@ from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/namespace.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input.cpp:1: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/overall_counts.cpp:1: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -14471,24 +14587,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/file_utils.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/input.cpp:3: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h: In function ‘scitbx::af::shared > scitbx::misc::split_lines(const char*, std::size_t, bool, bool)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:24:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 24 | while (i < size) { - | ~~^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:25:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 25 | while (i < size && data[i] != '\n' && data[i] != '\r') i++; - | ~~^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:27:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 27 | if (i < size) { - | ~~^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:28:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 28 | if (data[i] == '\r' && i+1 < size && data[i+1] == '\n') { - | ~~~~^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:46:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 46 | if (j < size) { - | ~~^~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -14550,8 +14648,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o iotbx/pdb/overall_counts.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/overall_counts.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/pdb/rna_dna_atom_names_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/rna_dna_atom_names_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/pdb/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/utils.cpp @@ -14564,66 +14660,6 @@ from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:31, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/namespace.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/hierarchy.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/overall_counts.cpp:1: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:31, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/namespace.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/write_utils.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/write_utils.cpp:1: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: @@ -14678,7 +14714,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o iotbx/pdb/hybrid_36_fem -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread iotbx/pdb/hybrid_36_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/write_utils.cpp: In destructor ‘iotbx::pdb::write_utils::fstream_open_close::~fstream_open_close()’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/write_utils.cpp:42:7: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 42 | throw std::runtime_error( @@ -14686,6 +14721,7 @@ 43 | "Failure writing to file: \"" + file_name + "\""); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/write_utils.cpp:42:7: note: in C++11 destructors default to ‘noexcept’ +g++ -o iotbx/pdb/hybrid_36_fem -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread iotbx/pdb/hybrid_36_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system g++ -o iotbx/pdb/xray_structure_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/xray_structure_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/shelx/shelx_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/shelx/shelx_ext.cpp @@ -14694,34 +14730,6 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o iotbx/xplor/boost_python/xplor_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/xplor/boost_python/xplor_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/xray_structure.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/xray_structure_bpl.cpp:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ - 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here - 203 | new tensor_rank_3_constraints_t(matrices_.const_ref(), 1, true)); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 185 | for (int j = 0; j < tensor_t::size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ - 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); - | ^~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here - 214 | new tensor_rank_4_constraints_t(matrices_.const_ref(), 1, true)); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 185 | for (int j = 0; j < tensor_t::size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~ g++ -o lib/libann_adaptor.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libann_adaptor.so.0 annlib_adaptbx/ann/ann_adaptor.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lann-cctbx /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14736,6 +14744,13 @@ 'lib/libann_adaptor.so.0'->'lib/libann_adaptor.so.0.0.1' 'lib/libann_adaptor.so'->'lib/libann_adaptor.so.0.0.1' g++ -o lib/annlib_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=annlib_ext.so.0 annlib_adaptbx/ann/boost_python/annlib_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lann-cctbx -lann_adaptor -lboost_thread -lboost_system -lboost_python313 -lm +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/xray/scatterer.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/xray_structure.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/pdb/xray_structure_bpl.cpp:7: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h: In member function ‘bool cctbx::sgtbx::site_symmetry_ops::contains(const cctbx::sgtbx::rt_mx&) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 100 | for (int i=0; i'lib/annlib_ext.so.0.0.1' 'lib/annlib_ext.so'->'lib/annlib_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_boost_thread_test_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_boost_thread_test_ext.so.0 boost_adaptbx/tests/boost_thread_test.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14757,11 +14772,31 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_breadth_first_search_ext.so.0 boost_adaptbx/graph/breadth_first_search_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm Create symlinks for: 'lib/boost_adaptbx_boost_thread_test_ext.so.0.0.1' 'lib/boost_adaptbx_boost_thread_test_ext.so.0'->'lib/boost_adaptbx_boost_thread_test_ext.so.0.0.1' 'lib/boost_adaptbx_boost_thread_test_ext.so'->'lib/boost_adaptbx_boost_thread_test_ext.so.0.0.1' -g++ -o lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_clustering_algorithm_ext.so.0 boost_adaptbx/graph/clustering_algorithm_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_breadth_first_search_ext.so.0 boost_adaptbx/graph/breadth_first_search_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:6: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ + 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:203:75: required from here + 203 | new tensor_rank_3_constraints_t(matrices_.const_ref(), 1, true)); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 185 | for (int j = 0; j < tensor_t::size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ + 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); + | ^~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:214:75: required from here + 214 | new tensor_rank_4_constraints_t(matrices_.const_ref(), 1, true)); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 185 | for (int j = 0; j < tensor_t::size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~ /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14770,6 +14805,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0'->'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_breadth_first_search_ext.so'->'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_clustering_algorithm_ext.so.0 boost_adaptbx/graph/clustering_algorithm_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14778,7 +14817,12 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0'->'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so'->'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_connected_component_algorithm_ext.so.0 boost_adaptbx/graph/connected_component_algorithm_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/boost_adaptbx_graph_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_ext.so.0 boost_adaptbx/graph/graph_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_graph_structure_comparison_ext.so.0 boost_adaptbx/graph/graph_structure_comparison_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14787,17 +14831,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0'->'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_breadth_first_search_ext.so'->'lib/boost_adaptbx_graph_breadth_first_search_ext.so.0.0.1' -g++ -o lib/boost_adaptbx_graph_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_ext.so.0 boost_adaptbx/graph/graph_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0'->'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so'->'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' -g++ -o lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_graph_structure_comparison_ext.so.0 boost_adaptbx/graph/graph_structure_comparison_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0'->'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_clustering_algorithm_ext.so'->'lib/boost_adaptbx_graph_clustering_algorithm_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14806,7 +14839,14 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0'->'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so'->'lib/boost_adaptbx_graph_connected_component_algorithm_ext.so.0.0.1' g++ -o lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_maximum_clique_ext.so.0 boost_adaptbx/graph/maximum_clique_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_graph_metric_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_metric_ext.so.0 boost_adaptbx/graph/metric_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14815,10 +14855,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so'->'lib/boost_adaptbx_graph_graph_structure_comparison_ext.so.0.0.1' -g++ -o lib/boost_adaptbx_graph_metric_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_metric_ext.so.0 boost_adaptbx/graph/metric_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_min_cut_max_flow_ext.so.0 boost_adaptbx/graph/min_cut_max_flow_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14835,10 +14872,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/boost_adaptbx_graph_metric_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_metric_ext.so.0'->'lib/boost_adaptbx_graph_metric_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_metric_ext.so'->'lib/boost_adaptbx_graph_metric_ext.so.0.0.1' -g++ -o lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_min_cut_max_flow_ext.so.0 boost_adaptbx/graph/min_cut_max_flow_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14847,13 +14880,17 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/boost_adaptbx_graph_metric_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_metric_ext.so.0'->'lib/boost_adaptbx_graph_metric_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_metric_ext.so'->'lib/boost_adaptbx_graph_metric_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_graph_utility_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_utility_ext.so.0 boost_adaptbx/graph/utility_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm Create symlinks for: 'lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1' 'lib/boost_adaptbx_graph_maximum_clique_ext.so.0'->'lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1' 'lib/boost_adaptbx_graph_maximum_clique_ext.so'->'lib/boost_adaptbx_graph_maximum_clique_ext.so.0.0.1' -g++ -o lib/boost_adaptbx_graph_utility_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_graph_utility_ext.so.0 boost_adaptbx/graph/utility_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/boost_adaptbx_graph_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_ext.so.0'->'lib/boost_adaptbx_graph_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_ext.so'->'lib/boost_adaptbx_graph_ext.so.0.0.1' +g++ -o lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_python_streambuf_test_ext.so.0 boost_adaptbx/tests/python_streambuf_test_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -lboost_timer +Create symlinks for: 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0'->'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so'->'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14862,15 +14899,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0'->'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so'->'lib/boost_adaptbx_graph_min_cut_max_flow_ext.so.0.0.1' -g++ -o lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_adaptbx_python_streambuf_test_ext.so.0 boost_adaptbx/tests/python_streambuf_test_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -lboost_timer g++ -o lib/boost_optional_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_optional_ext.so.0 boost_adaptbx/optional_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -lboost_timer -g++ -o lib/boost_python_hybrid_times_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_python_hybrid_times_ext.so.0 boost_adaptbx/hybrid_times_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/boost_adaptbx_graph_utility_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_utility_ext.so.0'->'lib/boost_adaptbx_graph_utility_ext.so.0.0.1' - 'lib/boost_adaptbx_graph_utility_ext.so'->'lib/boost_adaptbx_graph_utility_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14880,6 +14909,13 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1' + 'lib/boost_adaptbx_python_streambuf_test_ext.so.0'->'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1' + 'lib/boost_adaptbx_python_streambuf_test_ext.so'->'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1' +g++ -o lib/boost_python_hybrid_times_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_python_hybrid_times_ext.so.0 boost_adaptbx/hybrid_times_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/boost_adaptbx_graph_utility_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_utility_ext.so.0'->'lib/boost_adaptbx_graph_utility_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_utility_ext.so'->'lib/boost_adaptbx_graph_utility_ext.so.0.0.1' g++ -o lib/boost_python_meta_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_python_meta_ext.so.0 boost_adaptbx/meta_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -lboost_timer /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14898,14 +14934,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/boost_optional_ext.so.0.0.1' - 'lib/boost_optional_ext.so.0'->'lib/boost_optional_ext.so.0.0.1' - 'lib/boost_optional_ext.so'->'lib/boost_optional_ext.so.0.0.1' -g++ -o lib/boost_rational_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_rational_ext.so.0 boost_adaptbx/rational_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1' - 'lib/boost_adaptbx_python_streambuf_test_ext.so.0'->'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1' - 'lib/boost_adaptbx_python_streambuf_test_ext.so'->'lib/boost_adaptbx_python_streambuf_test_ext.so.0.0.1' -g++ -o lib/boost_tuple_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_tuple_ext.so.0 boost_adaptbx/tuple_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -lboost_timer /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14915,9 +14943,20 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/boost_optional_ext.so.0.0.1' + 'lib/boost_optional_ext.so.0'->'lib/boost_optional_ext.so.0.0.1' + 'lib/boost_optional_ext.so'->'lib/boost_optional_ext.so.0.0.1' +g++ -o lib/boost_rational_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_rational_ext.so.0 boost_adaptbx/rational_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm Create symlinks for: 'lib/boost_python_hybrid_times_ext.so.0.0.1' 'lib/boost_python_hybrid_times_ext.so.0'->'lib/boost_python_hybrid_times_ext.so.0.0.1' 'lib/boost_python_hybrid_times_ext.so'->'lib/boost_python_hybrid_times_ext.so.0.0.1' +g++ -o lib/boost_tuple_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=boost_tuple_ext.so.0 boost_adaptbx/tuple_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -lboost_timer +Create symlinks for: 'lib/boost_python_meta_ext.so.0.0.1' + 'lib/boost_python_meta_ext.so.0'->'lib/boost_python_meta_ext.so.0.0.1' + 'lib/boost_python_meta_ext.so'->'lib/boost_python_meta_ext.so.0.0.1' +Create symlinks for: 'lib/boost_adaptbx_graph_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_ext.so.0'->'lib/boost_adaptbx_graph_ext.so.0.0.1' + 'lib/boost_adaptbx_graph_ext.so'->'lib/boost_adaptbx_graph_ext.so.0.0.1' g++ -o lib/cbflib_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cbflib_ext.so.0 cbflib_adaptbx/detectors/boost_python/cbflib_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lcbf-private -lcbf -lboost_thread -lboost_system -lboost_python313 -lm -lhdf5 /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14927,6 +14966,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/libccp4io.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libccp4io.so.0 ccp4io_adaptbx/fortran_call_stubs.o ccp4io_adaptbx/printf_wrappers.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lm -lccp4c /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14936,46 +14976,37 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/boost_rational_ext.so.0.0.1' + 'lib/boost_rational_ext.so.0'->'lib/boost_rational_ext.so.0.0.1' + 'lib/boost_rational_ext.so'->'lib/boost_rational_ext.so.0.0.1' +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/boost_python_meta_ext.so.0.0.1' - 'lib/boost_python_meta_ext.so.0'->'lib/boost_python_meta_ext.so.0.0.1' - 'lib/boost_python_meta_ext.so'->'lib/boost_python_meta_ext.so.0.0.1' /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/libccp4io.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libccp4io.so.0 ccp4io_adaptbx/fortran_call_stubs.o ccp4io_adaptbx/printf_wrappers.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lm -lccp4c -Create symlinks for: 'lib/boost_rational_ext.so.0.0.1' - 'lib/boost_rational_ext.so.0'->'lib/boost_rational_ext.so.0.0.1' - 'lib/boost_rational_ext.so'->'lib/boost_rational_ext.so.0.0.1' Create symlinks for: 'lib/boost_tuple_ext.so.0.0.1' 'lib/boost_tuple_ext.so.0'->'lib/boost_tuple_ext.so.0.0.1' 'lib/boost_tuple_ext.so'->'lib/boost_tuple_ext.so.0.0.1' -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.sog++ -o scitbx/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/utils.cpp -: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/libccp4io.so.0.0.1' + 'lib/libccp4io.so.0'->'lib/libccp4io.so.0.0.1' + 'lib/libccp4io.so'->'lib/libccp4io.so.0.0.1' +g++ -o scitbx/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/utils.cpp /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/cbflib_ext.so.0.0.1' - 'lib/cbflib_ext.so.0'->'lib/cbflib_ext.so.0.0.1' - 'lib/cbflib_ext.so'->'lib/cbflib_ext.so.0.0.1' g++ -o scitbx/boost_python/slice.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/slice.cpp -Create symlinks for: 'lib/libccp4io.so.0.0.1' - 'lib/libccp4io.so.0'->'lib/libccp4io.so.0.0.1' - 'lib/libccp4io.so'->'lib/libccp4io.so.0.0.1' -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/array_family/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/utils.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/ccp4io_adaptbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=ccp4io_adaptbx_ext.so.0 ccp4io_adaptbx/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lccp4io -lccp4c -lssm -lmmdb2 -lboost_thread -lboost_system -lboost_python313 -lm +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /usr/lib/aarch64-linux-gnu/libssm.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libmmdb2.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -14986,17 +15017,16 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/cbflib_ext.so.0.0.1' + 'lib/cbflib_ext.so.0'->'lib/cbflib_ext.so.0.0.1' + 'lib/cbflib_ext.so'->'lib/cbflib_ext.so.0.0.1' Create symlinks for: 'lib/ccp4io_adaptbx_ext.so.0.0.1' 'lib/ccp4io_adaptbx_ext.so.0'->'lib/ccp4io_adaptbx_ext.so.0.0.1' 'lib/ccp4io_adaptbx_ext.so'->'lib/ccp4io_adaptbx_ext.so.0.0.1' +g++ -o scitbx/array_family/boost_python/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/utils.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/cma_es_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cma_es_ext.so.0 cma_es/cma_es_ext.o cma_es/cma/cmaes.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm g++ -o lib/dxtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_ext.so.0 dxtbx/src/dxtbx/boost_python/ext.o dxtbx/src/dxtbx/boost_python/compression.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15005,21 +15035,16 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/dxtbx_ext.so.0.0.1' - 'lib/dxtbx_ext.so.0'->'lib/dxtbx_ext.so.0.0.1' - 'lib/dxtbx_ext.so'->'lib/dxtbx_ext.so.0.0.1' -g++ -o lib/dxtbx_format_image_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_format_image_ext.so.0 dxtbx/src/dxtbx/format/boost_python/image_ext.o dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lhdf5 Create symlinks for: 'lib/cma_es_ext.so.0.0.1' 'lib/cma_es_ext.so.0'->'lib/cma_es_ext.so.0.0.1' 'lib/cma_es_ext.so'->'lib/cma_es_ext.so.0.0.1' -g++ -o lib/dxtbx_format_nexus_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_format_nexus_ext.so.0 dxtbx/src/dxtbx/format/boost_python/nexus_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lhdf5 /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/dxtbx_format_image_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_format_image_ext.so.0 dxtbx/src/dxtbx/format/boost_python/image_ext.o dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lhdf5 /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15027,44 +15052,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/dxtbx_format_nexus_ext.so.0.0.1' - 'lib/dxtbx_format_nexus_ext.so.0'->'lib/dxtbx_format_nexus_ext.so.0.0.1' - 'lib/dxtbx_format_nexus_ext.so'->'lib/dxtbx_format_nexus_ext.so.0.0.1' -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/utils.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/utils.cpp:1: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/fable_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=fable_ext.so.0 fable/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/dxtbx_ext.so.0.0.1' + 'lib/dxtbx_ext.so.0'->'lib/dxtbx_ext.so.0.0.1' + 'lib/dxtbx_ext.so'->'lib/dxtbx_ext.so.0.0.1' +g++ -o lib/dxtbx_format_nexus_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_format_nexus_ext.so.0 dxtbx/src/dxtbx/format/boost_python/nexus_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lhdf5 In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, @@ -15105,6 +15096,51 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +Create symlinks for: 'lib/dxtbx_format_image_ext.so.0.0.1' + 'lib/dxtbx_format_image_ext.so.0'->'lib/dxtbx_format_image_ext.so.0.0.1' + 'lib/dxtbx_format_image_ext.so'->'lib/dxtbx_format_image_ext.so.0.0.1' +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/utils.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/utils.cpp:1: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o lib/fable_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=fable_ext.so.0 fable/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -15183,6 +15219,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o lib/iotbx_ccp4_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_ccp4_map_ext.so.0 iotbx/ccp4_map/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lccp4c -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/dxtbx_format_nexus_ext.so.0.0.1' + 'lib/dxtbx_format_nexus_ext.so.0'->'lib/dxtbx_format_nexus_ext.so.0.0.1' + 'lib/dxtbx_format_nexus_ext.so'->'lib/dxtbx_format_nexus_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15191,16 +15231,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/dxtbx_format_image_ext.so.0.0.1' - 'lib/dxtbx_format_image_ext.so.0'->'lib/dxtbx_format_image_ext.so.0.0.1' - 'lib/dxtbx_format_image_ext.so'->'lib/dxtbx_format_image_ext.so.0.0.1' -g++ -o lib/iotbx_ccp4_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_ccp4_map_ext.so.0 iotbx/ccp4_map/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lccp4c -lboost_thread -lboost_system -lboost_python313 -lm g++ -o ucif/cifParser.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/ucif/cifParser.cpp -Create symlinks for: 'lib/fable_ext.so.0.0.1' - 'lib/fable_ext.so.0'->'lib/fable_ext.so.0.0.1' - 'lib/fable_ext.so'->'lib/fable_ext.so.0.0.1' -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o ucif/cifLexer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/ucif/cifLexer.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15210,7 +15241,16 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/fable_ext.so.0.0.1' + 'lib/fable_ext.so.0'->'lib/fable_ext.so.0.0.1' + 'lib/fable_ext.so'->'lib/fable_ext.so.0.0.1' +g++ -o ucif/cifLexer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/ucif/cifLexer.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/iotbx_detectors_bruker_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_detectors_bruker_ext.so.0 iotbx/detectors/bruker_ext.o iotbx/detectors/bruker.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/iotbx_ccp4_map_ext.so.0.0.1' + 'lib/iotbx_ccp4_map_ext.so.0'->'lib/iotbx_ccp4_map_ext.so.0.0.1' + 'lib/iotbx_ccp4_map_ext.so'->'lib/iotbx_ccp4_map_ext.so.0.0.1' +g++ -o lib/iotbx_detectors_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_detectors_ext.so.0 iotbx/detectors/detectors_ext.o iotbx/detectors/image_divider.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15219,14 +15259,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/iotbx_ccp4_map_ext.so.0.0.1' - 'lib/iotbx_ccp4_map_ext.so.0'->'lib/iotbx_ccp4_map_ext.so.0.0.1' - 'lib/iotbx_ccp4_map_ext.so'->'lib/iotbx_ccp4_map_ext.so.0.0.1' -g++ -o lib/iotbx_detectors_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_detectors_ext.so.0 iotbx/detectors/detectors_ext.o iotbx/detectors/image_divider.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/iotbx_detectors_bruker_ext.so.0.0.1' - 'lib/iotbx_detectors_bruker_ext.so.0'->'lib/iotbx_detectors_bruker_ext.so.0.0.1' - 'lib/iotbx_detectors_bruker_ext.so'->'lib/iotbx_detectors_bruker_ext.so.0.0.1' -g++ -o lib/iotbx_dsn6_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_dsn6_map_ext.so.0 iotbx/dsn6/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15235,6 +15267,11 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/iotbx_detectors_bruker_ext.so.0.0.1' + 'lib/iotbx_detectors_bruker_ext.so.0'->'lib/iotbx_detectors_bruker_ext.so.0.0.1' + 'lib/iotbx_detectors_bruker_ext.so'->'lib/iotbx_detectors_bruker_ext.so.0.0.1' +g++ -o lib/iotbx_dsn6_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_dsn6_map_ext.so.0 iotbx/dsn6/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/iotbx_dtrek_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_dtrek_ext.so.0 iotbx/misc/boost_python/dtrek_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15246,11 +15283,10 @@ Create symlinks for: 'lib/iotbx_dsn6_map_ext.so.0.0.1' 'lib/iotbx_dsn6_map_ext.so.0'->'lib/iotbx_dsn6_map_ext.so.0.0.1' 'lib/iotbx_dsn6_map_ext.so'->'lib/iotbx_dsn6_map_ext.so.0.0.1' -g++ -o lib/iotbx_dtrek_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_dtrek_ext.so.0 iotbx/misc/boost_python/dtrek_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/libiotbx_mtz.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libiotbx_mtz.so.0 iotbx/mtz/object.o iotbx/mtz/crystal.o iotbx/mtz/dataset.o iotbx/mtz/column.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lccp4io -lccp4c -lm -lboost_thread -lboost_system Create symlinks for: 'lib/iotbx_detectors_ext.so.0.0.1' 'lib/iotbx_detectors_ext.so.0'->'lib/iotbx_detectors_ext.so.0.0.1' 'lib/iotbx_detectors_ext.so'->'lib/iotbx_detectors_ext.so.0.0.1' -g++ -o lib/libiotbx_mtz.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libiotbx_mtz.so.0 iotbx/mtz/object.o iotbx/mtz/crystal.o iotbx/mtz/dataset.o iotbx/mtz/column.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lccp4io -lccp4c -lm -lboost_thread -lboost_system /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15259,9 +15295,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/iotbx_dtrek_ext.so.0.0.1' - 'lib/iotbx_dtrek_ext.so.0'->'lib/iotbx_dtrek_ext.so.0.0.1' - 'lib/iotbx_dtrek_ext.so'->'lib/iotbx_dtrek_ext.so.0.0.1' +g++ -o lib/iotbx_scalepack_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_scalepack_ext.so.0 iotbx/misc/boost_python/scalepack_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15270,7 +15304,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/iotbx_scalepack_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_scalepack_ext.so.0 iotbx/misc/boost_python/scalepack_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/iotbx_dtrek_ext.so.0.0.1' + 'lib/iotbx_dtrek_ext.so.0'->'lib/iotbx_dtrek_ext.so.0.0.1' + 'lib/iotbx_dtrek_ext.so'->'lib/iotbx_dtrek_ext.so.0.0.1' g++ -o lib/iotbx_shelx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_shelx_ext.so.0 iotbx/shelx/shelx_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15280,6 +15316,13 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/libiotbx_mtz.so.0.0.1' + 'lib/libiotbx_mtz.so.0'->'lib/libiotbx_mtz.so.0.0.1' + 'lib/libiotbx_mtz.so'->'lib/libiotbx_mtz.so.0.0.1' +g++ -o lib/iotbx_wildcard_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_wildcard_ext.so.0 iotbx/wildcard_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/iotbx_scalepack_ext.so.0.0.1' + 'lib/iotbx_scalepack_ext.so.0'->'lib/iotbx_scalepack_ext.so.0.0.1' + 'lib/iotbx_scalepack_ext.so'->'lib/iotbx_scalepack_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15288,13 +15331,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/libiotbx_mtz.so.0.0.1' - 'lib/libiotbx_mtz.so.0'->'lib/libiotbx_mtz.so.0.0.1' - 'lib/libiotbx_mtz.so'->'lib/libiotbx_mtz.so.0.0.1' -g++ -o lib/iotbx_wildcard_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_wildcard_ext.so.0 iotbx/wildcard_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/iotbx_shelx_ext.so.0.0.1' - 'lib/iotbx_shelx_ext.so.0'->'lib/iotbx_shelx_ext.so.0.0.1' - 'lib/iotbx_shelx_ext.so'->'lib/iotbx_shelx_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15303,9 +15339,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/iotbx_scalepack_ext.so.0.0.1' - 'lib/iotbx_scalepack_ext.so.0'->'lib/iotbx_scalepack_ext.so.0.0.1' - 'lib/iotbx_scalepack_ext.so'->'lib/iotbx_scalepack_ext.so.0.0.1' +Create symlinks for: 'lib/iotbx_shelx_ext.so.0.0.1' + 'lib/iotbx_shelx_ext.so.0'->'lib/iotbx_shelx_ext.so.0.0.1' + 'lib/iotbx_shelx_ext.so'->'lib/iotbx_shelx_ext.so.0.0.1' Create symlinks for: 'lib/iotbx_wildcard_ext.so.0.0.1' 'lib/iotbx_wildcard_ext.so.0'->'lib/iotbx_wildcard_ext.so.0.0.1' 'lib/iotbx_wildcard_ext.so'->'lib/iotbx_wildcard_ext.so.0.0.1' @@ -15317,6 +15353,8 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o spotfinder/core_toolbox/libdistl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/libdistl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o spotfinder/core_toolbox/hough.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/hough.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/iotbx_cif_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_cif_ext.so.0 iotbx/cif/boost_python/cif_ext.o ucif/cifParser.o ucif/cifLexer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -lm -lantlr3c /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15327,15 +15365,14 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o spotfinder/core_toolbox/distl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/distl.cpp +g++ -o lib/libscitbx_boost_python.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -shared -rdynamic -std=c++14 -Wl,-soname=libscitbx_boost_python.so.0 scitbx/boost_python/utils.o scitbx/boost_python/slice.o scitbx/array_family/boost_python/utils.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/iotbx_cif_ext.so.0.0.1' 'lib/iotbx_cif_ext.so.0'->'lib/iotbx_cif_ext.so.0.0.1' 'lib/iotbx_cif_ext.so'->'lib/iotbx_cif_ext.so.0.0.1' -g++ -o spotfinder/core_toolbox/hough.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/hough.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o spotfinder/core_toolbox/distl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/distl.cpp +g++ -o spotfinder/core_toolbox/spotfilter.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/spotfilter.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/libscitbx_boost_python.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -shared -rdynamic -std=c++14 -Wl,-soname=libscitbx_boost_python.so.0 scitbx/boost_python/utils.o scitbx/boost_python/slice.o scitbx/array_family/boost_python/utils.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lboost_python313 -g++ -o lib/iotbx_xplor_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_xplor_ext.so.0 iotbx/xplor/boost_python/xplor_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_xplor -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15345,23 +15382,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. Create symlinks for: 'lib/libscitbx_boost_python.so.0.0.1' 'lib/libscitbx_boost_python.so.0'->'lib/libscitbx_boost_python.so.0.0.1' 'lib/libscitbx_boost_python.so'->'lib/libscitbx_boost_python.so.0.0.1' -g++ -o lib/cctbx_statistics_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_statistics_ext.so.0 cctbx/boost_python/statistics_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/iotbx_xplor_ext.so.0.0.1' - 'lib/iotbx_xplor_ext.so.0'->'lib/iotbx_xplor_ext.so.0.0.1' - 'lib/iotbx_xplor_ext.so'->'lib/iotbx_xplor_ext.so.0.0.1' -g++ -o lib/cctbx_orientation_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_orientation_ext.so.0 cctbx/boost_python/orientation_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_adp_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_adp_restraints_ext.so.0 cctbx/adp_restraints/adp_restraints_bpl.o cctbx/adp_restraints/adp_restraints_ext.o cctbx/adp_restraints/rigid_bond_bpl.o cctbx/adp_restraints/rigu_bpl.o cctbx/adp_restraints/adp_similarity_bpl.o cctbx/adp_restraints/isotropic_adp_bpl.o cctbx/adp_restraints/aniso_restraints_bpl.o cctbx/adp_restraints/fixed_u_eq_adp_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_chemical_elements_ext.so.0 cctbx/eltbx/boost_python/chemical_elements_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15370,6 +15394,11 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1' + 'lib/cctbx_eltbx_chemical_elements_ext.so.0'->'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1' + 'lib/cctbx_eltbx_chemical_elements_ext.so'->'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1' +g++ -o lib/dxtbx_model_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_model_ext.so.0 dxtbx/src/dxtbx/model/boost_python/beam.o dxtbx/src/dxtbx/model/boost_python/spectrum.o dxtbx/src/dxtbx/model/boost_python/goniometer.o dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.o dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.o dxtbx/src/dxtbx/model/boost_python/panel.o dxtbx/src/dxtbx/model/boost_python/detector.o dxtbx/src/dxtbx/model/boost_python/scan.o dxtbx/src/dxtbx/model/boost_python/scan_helpers.o dxtbx/src/dxtbx/model/boost_python/crystal.o dxtbx/src/dxtbx/model/boost_python/parallax_correction.o dxtbx/src/dxtbx/model/boost_python/pixel_to_millimeter.o dxtbx/src/dxtbx/model/boost_python/experiment.o dxtbx/src/dxtbx/model/boost_python/experiment_list.o dxtbx/src/dxtbx/model/boost_python/model_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python313 -lcbf -lhdf5 +g++ -o lib/iotbx_xplor_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_xplor_ext.so.0 iotbx/xplor/boost_python/xplor_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_xplor -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15378,10 +15407,11 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_statistics_ext.so.0.0.1' - 'lib/cctbx_statistics_ext.so.0'->'lib/cctbx_statistics_ext.so.0.0.1' - 'lib/cctbx_statistics_ext.so'->'lib/cctbx_statistics_ext.so.0.0.1' -g++ -o lib/cctbx_eltbx_sasaki_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_sasaki_ext.so.0 cctbx/eltbx/boost_python/sasaki_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_symmetry_search_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_symmetry_search_ext.so.0 cctbx/symmetry_search/boost_python/symmetry_search_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/iotbx_xplor_ext.so.0.0.1' + 'lib/iotbx_xplor_ext.so.0'->'lib/iotbx_xplor_ext.so.0.0.1' + 'lib/iotbx_xplor_ext.so'->'lib/iotbx_xplor_ext.so.0.0.1' +g++ -o lib/cctbx_geometry_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_geometry_ext.so.0 cctbx/geometry/boost_python/geometry_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15390,10 +15420,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_orientation_ext.so.0.0.1' - 'lib/cctbx_orientation_ext.so.0'->'lib/cctbx_orientation_ext.so.0.0.1' - 'lib/cctbx_orientation_ext.so'->'lib/cctbx_orientation_ext.so.0.0.1' -g++ -o lib/cctbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_array_family_flex_ext.so.0 cctbx/array_family/boost_python/flex_ext.o cctbx/array_family/boost_python/flex_hendrickson_lattman.o cctbx/array_family/boost_python/flex_miller_index.o cctbx/array_family/boost_python/flex_xray_scatterer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15402,10 +15428,14 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' - 'lib/cctbx_eltbx_sasaki_ext.so.0'->'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' - 'lib/cctbx_eltbx_sasaki_ext.so'->'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' -g++ -o lib/gltbx_fonts_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_fonts_ext.so.0 gltbx/fonts_ext.o gltbx/font_ucs_8x13.o gltbx/font_ucs_9x15.o gltbx/font_ucs_10x20.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm +Create symlinks for: 'lib/cctbx_symmetry_search_ext.so.0.0.1' + 'lib/cctbx_symmetry_search_ext.so.0'->'lib/cctbx_symmetry_search_ext.so.0.0.1' + 'lib/cctbx_symmetry_search_ext.so'->'lib/cctbx_symmetry_search_ext.so.0.0.1' +g++ -o lib/cctbx_anharmonic_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_anharmonic_ext.so.0 cctbx/adptbx/boost_python/anharmonic_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_geometry_ext.so.0.0.1' + 'lib/cctbx_geometry_ext.so.0'->'lib/cctbx_geometry_ext.so.0.0.1' + 'lib/cctbx_geometry_ext.so'->'lib/cctbx_geometry_ext.so.0.0.1' +g++ -o lib/gltbx_glu_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_glu_ext.so.0 gltbx/glu_ext.o gltbx/glu_defines_00_bpl.o gltbx/glu_defines_01_bpl.o gltbx/glu_functions_00_bpl.o gltbx/glu_functions_01_bpl.o gltbx/glu_functions_02_bpl.o gltbx/glu_functions_03_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15424,38 +15454,33 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/dxtbx_model_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_model_ext.so.0 dxtbx/src/dxtbx/model/boost_python/beam.o dxtbx/src/dxtbx/model/boost_python/spectrum.o dxtbx/src/dxtbx/model/boost_python/goniometer.o dxtbx/src/dxtbx/model/boost_python/kappa_goniometer.o dxtbx/src/dxtbx/model/boost_python/multi_axis_goniometer.o dxtbx/src/dxtbx/model/boost_python/panel.o dxtbx/src/dxtbx/model/boost_python/detector.o dxtbx/src/dxtbx/model/boost_python/scan.o dxtbx/src/dxtbx/model/boost_python/scan_helpers.o dxtbx/src/dxtbx/model/boost_python/crystal.o dxtbx/src/dxtbx/model/boost_python/parallax_correction.o dxtbx/src/dxtbx/model/boost_python/pixel_to_millimeter.o dxtbx/src/dxtbx/model/boost_python/experiment.o dxtbx/src/dxtbx/model/boost_python/experiment_list.o dxtbx/src/dxtbx/model/boost_python/model_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python313 -lcbf -lhdf5 -Create symlinks for: 'lib/gltbx_fonts_ext.so.0.0.1' - 'lib/gltbx_fonts_ext.so.0'->'lib/gltbx_fonts_ext.so.0.0.1' - 'lib/gltbx_fonts_ext.so'->'lib/gltbx_fonts_ext.so.0.0.1' -g++ -o lib/cctbx_translation_search_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_translation_search_ext.so.0 cctbx/translation_search/boost_python/translation_search_ext.o cctbx/translation_search/boost_python/fast_nv1995.o cctbx/translation_search/boost_python/fast_terms.o cctbx/translation_search/boost_python/symmetry_flags.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_anharmonic_ext.so.0.0.1' + 'lib/cctbx_anharmonic_ext.so.0'->'lib/cctbx_anharmonic_ext.so.0.0.1' + 'lib/cctbx_anharmonic_ext.so'->'lib/cctbx_anharmonic_ext.so.0.0.1' +g++ -o lib/cctbx_xray_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_xray_ext.so.0 cctbx/xray/boost_python/xray_ext.o cctbx/xray/boost_python/conversions.o cctbx/xray/boost_python/gradient_flags.o cctbx/xray/boost_python/gradients_direct.o cctbx/xray/boost_python/each_hkl_gradients_direct.o cctbx/xray/boost_python/fast_gradients.o cctbx/xray/boost_python/minimization.o cctbx/xray/boost_python/scatterer_flags.o cctbx/xray/boost_python/scatterer.o cctbx/xray/boost_python/scattering_type_registry.o cctbx/xray/boost_python/sampling_base.o cctbx/xray/boost_python/sampled_model_density.o cctbx/xray/boost_python/structure_factors_direct.o cctbx/xray/boost_python/structure_factors_simple.o cctbx/xray/boost_python/curvatures_simple.o cctbx/xray/boost_python/targets.o cctbx/xray/boost_python/f_model_bpl.o cctbx/xray/boost_python/twin_targets.o cctbx/xray/boost_python/grouped_data.o cctbx/xray/boost_python/parameter_map.o cctbx/xray/boost_python/twin_components.o cctbx/xray/boost_python/extinction.o cctbx/xray/boost_python/sigmaa.o cctbx/xray/targets/shelxl_wght_ls_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/libiotbx_pdb.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libiotbx_pdb.so.0 iotbx/pdb/hybrid_36_c.o iotbx/pdb/hybrid_36_cpp.o iotbx/pdb/utils.o iotbx/pdb/write_utils.o iotbx/pdb/hierarchy.o iotbx/pdb/hierarchy_select.o iotbx/pdb/hierarchy_atoms.o iotbx/pdb/construct_hierarchy.o iotbx/pdb/overall_counts.o iotbx/pdb/hierarchy_write.o iotbx/pdb/atom_selection.o iotbx/pdb/input.o iotbx/pdb/input_write.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +Create symlinks for: 'lib/gltbx_glu_ext.so.0.0.1' + 'lib/gltbx_glu_ext.so.0'->'lib/gltbx_glu_ext.so.0.0.1' + 'lib/gltbx_glu_ext.so'->'lib/gltbx_glu_ext.so.0.0.1' +g++ -o lib/gltbx_viewer_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_viewer_utils_ext.so.0 gltbx/viewer_utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_adp_restraints_ext.so.0.0.1' - 'lib/cctbx_adp_restraints_ext.so.0'->'lib/cctbx_adp_restraints_ext.so.0.0.1' - 'lib/cctbx_adp_restraints_ext.so'->'lib/cctbx_adp_restraints_ext.so.0.0.1' -g++ -o lib/determine_unit_cell_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=determine_unit_cell_ext.so.0 cctbx/uctbx/determine_unit_cell/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/cctbx_translation_search_ext.so.0.0.1' - 'lib/cctbx_translation_search_ext.so.0'->'lib/cctbx_translation_search_ext.so.0.0.1' - 'lib/cctbx_translation_search_ext.so'->'lib/cctbx_translation_search_ext.so.0.0.1' -g++ -o lib/cctbx_xray_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_xray_ext.so.0 cctbx/xray/boost_python/xray_ext.o cctbx/xray/boost_python/conversions.o cctbx/xray/boost_python/gradient_flags.o cctbx/xray/boost_python/gradients_direct.o cctbx/xray/boost_python/each_hkl_gradients_direct.o cctbx/xray/boost_python/fast_gradients.o cctbx/xray/boost_python/minimization.o cctbx/xray/boost_python/scatterer_flags.o cctbx/xray/boost_python/scatterer.o cctbx/xray/boost_python/scattering_type_registry.o cctbx/xray/boost_python/sampling_base.o cctbx/xray/boost_python/sampled_model_density.o cctbx/xray/boost_python/structure_factors_direct.o cctbx/xray/boost_python/structure_factors_simple.o cctbx/xray/boost_python/curvatures_simple.o cctbx/xray/boost_python/targets.o cctbx/xray/boost_python/f_model_bpl.o cctbx/xray/boost_python/twin_targets.o cctbx/xray/boost_python/grouped_data.o cctbx/xray/boost_python/parameter_map.o cctbx/xray/boost_python/twin_components.o cctbx/xray/boost_python/extinction.o cctbx/xray/boost_python/sigmaa.o cctbx/xray/targets/shelxl_wght_ls_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_array_family_flex_ext.so.0.0.1' - 'lib/cctbx_array_family_flex_ext.so.0'->'lib/cctbx_array_family_flex_ext.so.0.0.1' - 'lib/cctbx_array_family_flex_ext.so'->'lib/cctbx_array_family_flex_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15468,12 +15493,13 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_icsd_radii_ext.so.0 cctbx/eltbx/boost_python/icsd_radii_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/determine_unit_cell_ext.so.0.0.1' - 'lib/determine_unit_cell_ext.so.0'->'lib/determine_unit_cell_ext.so.0.0.1' - 'lib/determine_unit_cell_ext.so'->'lib/determine_unit_cell_ext.so.0.0.1' -g++ -o lib/libiotbx_pdb.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libiotbx_pdb.so.0 iotbx/pdb/hybrid_36_c.o iotbx/pdb/hybrid_36_cpp.o iotbx/pdb/utils.o iotbx/pdb/write_utils.o iotbx/pdb/hierarchy.o iotbx/pdb/hierarchy_select.o iotbx/pdb/hierarchy_atoms.o iotbx/pdb/construct_hierarchy.o iotbx/pdb/overall_counts.o iotbx/pdb/hierarchy_write.o iotbx/pdb/atom_selection.o iotbx/pdb/input.o iotbx/pdb/input_write.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -g++ -o lib/cctbx_dmtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_dmtbx_ext.so.0 cctbx/dmtbx/boost_python/dmtbx_ext.o cctbx/dmtbx/boost_python/triplet_phase_relation.o cctbx/dmtbx/boost_python/triplet_generator.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/gltbx_viewer_utils_ext.so.0.0.1' + 'lib/gltbx_viewer_utils_ext.so.0'->'lib/gltbx_viewer_utils_ext.so.0.0.1' + 'lib/gltbx_viewer_utils_ext.so'->'lib/gltbx_viewer_utils_ext.so.0.0.1' +g++ -o lib/gltbx_gl_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_gl_ext.so.0 gltbx/gl_ext.o gltbx/gl_defines_00_bpl.o gltbx/gl_defines_01_bpl.o gltbx/gl_defines_02_bpl.o gltbx/gl_defines_03_bpl.o gltbx/gl_defines_04_bpl.o gltbx/gl_defines_05_bpl.o gltbx/gl_defines_06_bpl.o gltbx/gl_defines_07_bpl.o gltbx/gl_functions_00_bpl.o gltbx/gl_functions_01_bpl.o gltbx/gl_functions_02_bpl.o gltbx/gl_functions_03_bpl.o gltbx/gl_functions_04_bpl.o gltbx/gl_functions_05_bpl.o gltbx/gl_functions_06_bpl.o gltbx/gl_functions_07_bpl.o gltbx/gl_functions_08_bpl.o gltbx/gl_functions_09_bpl.o gltbx/gl_functions_10_bpl.o gltbx/gl_functions_11_bpl.o gltbx/gl_functions_12_bpl.o gltbx/gl_functions_13_bpl.o gltbx/gl_functions_14_bpl.o gltbx/gl_functions_15_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm +Create symlinks for: 'lib/libiotbx_pdb.so.0.0.1' + 'lib/libiotbx_pdb.so.0'->'lib/libiotbx_pdb.so.0.0.1' + 'lib/libiotbx_pdb.so'->'lib/libiotbx_pdb.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15482,9 +15508,12 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/iotbx_pdb_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_pdb_ext.so.0 iotbx/pdb/ext.o iotbx/pdb/hybrid_36_bpl.o iotbx/pdb/common_residue_names_bpl.o iotbx/pdb/rna_dna_atom_names_bpl.o iotbx/pdb/input_bpl.o iotbx/pdb/xray_structure_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15498,23 +15527,22 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1' - 'lib/cctbx_eltbx_icsd_radii_ext.so.0'->'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1' - 'lib/cctbx_eltbx_icsd_radii_ext.so'->'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1' -g++ -o lib/cctbx_sgtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_sgtbx_ext.so.0 cctbx/sgtbx/boost_python/sgtbx_ext.o cctbx/sgtbx/boost_python/brick.o cctbx/sgtbx/boost_python/change_of_basis.o cctbx/sgtbx/boost_python/find_affine.o cctbx/sgtbx/boost_python/lattice_symmetry.o cctbx/sgtbx/boost_python/phase_info.o cctbx/sgtbx/boost_python/reciprocal_space_asu.o cctbx/sgtbx/boost_python/rot_mx.o cctbx/sgtbx/boost_python/rt_mx.o cctbx/sgtbx/boost_python/search_symmetry.o cctbx/sgtbx/boost_python/seminvariant.o cctbx/sgtbx/boost_python/site_symmetry.o cctbx/sgtbx/boost_python/space_group.o cctbx/sgtbx/boost_python/space_group_type.o cctbx/sgtbx/boost_python/sym_equiv_sites.o cctbx/sgtbx/boost_python/symbols.o cctbx/sgtbx/boost_python/tensor_rank_2.o cctbx/sgtbx/boost_python/tensors.o cctbx/sgtbx/boost_python/tr_vec.o cctbx/sgtbx/boost_python/wyckoff.o cctbx/sgtbx/boost_python/select_generators.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/cctbx_eltbx_henke_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_henke_ext.so.0 cctbx/eltbx/boost_python/henke_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/iotbx_pdb_ext.so.0.0.1' + 'lib/iotbx_pdb_ext.so.0'->'lib/iotbx_pdb_ext.so.0.0.1' + 'lib/iotbx_pdb_ext.so'->'lib/iotbx_pdb_ext.so.0.0.1' +g++ -o lib/cctbx_uctbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_uctbx_ext.so.0 cctbx/uctbx/boost_python/uctbx_ext.o cctbx/uctbx/boost_python/fast_minimum_reduction.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_dmtbx_ext.so.0.0.1' - 'lib/cctbx_dmtbx_ext.so.0'->'lib/cctbx_dmtbx_ext.so.0.0.1' - 'lib/cctbx_dmtbx_ext.so'->'lib/cctbx_dmtbx_ext.so.0.0.1' -g++ -o lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_fp_fdp_ext.so.0 cctbx/eltbx/boost_python/fp_fdp_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_symmetry_search_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_symmetry_search_ext.so.0 cctbx/symmetry_search/boost_python/symmetry_search_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/gltbx_gl_ext.so.0.0.1' + 'lib/gltbx_gl_ext.so.0'->'lib/gltbx_gl_ext.so.0.0.1' + 'lib/gltbx_gl_ext.so'->'lib/gltbx_gl_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15523,6 +15551,11 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/cctbx_eltbx_henke_ext.so.0.0.1' + 'lib/cctbx_eltbx_henke_ext.so.0'->'lib/cctbx_eltbx_henke_ext.so.0.0.1' + 'lib/cctbx_eltbx_henke_ext.so'->'lib/cctbx_eltbx_henke_ext.so.0.0.1' +g++ -o lib/cctbx_math_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_math_ext.so.0 cctbx/math/boost_python/math_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_emma_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_emma_ext.so.0 cctbx/boost_python/emma_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15531,23 +15564,17 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1' - 'lib/cctbx_eltbx_fp_fdp_ext.so.0'->'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1' - 'lib/cctbx_eltbx_fp_fdp_ext.so'->'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1' -g++ -o lib/gltbx_util_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_util_ext.so.0 gltbx/util_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm -Create symlinks for: 'lib/libiotbx_pdb.so.0.0.1' - 'lib/libiotbx_pdb.so.0'->'lib/libiotbx_pdb.so.0.0.1' - 'lib/libiotbx_pdb.so'->'lib/libiotbx_pdb.so.0.0.1' -Create symlinks for: 'lib/cctbx_symmetry_search_ext.so.0.0.1' - 'lib/cctbx_symmetry_search_ext.so.0'->'lib/cctbx_symmetry_search_ext.so.0.0.1' - 'lib/cctbx_symmetry_search_ext.so'->'lib/cctbx_symmetry_search_ext.so.0.0.1' -g++ -o lib/iotbx_pdb_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_pdb_ext.so.0 iotbx/pdb/ext.o iotbx/pdb/hybrid_36_bpl.o iotbx/pdb/common_residue_names_bpl.o iotbx/pdb/rna_dna_atom_names_bpl.o iotbx/pdb/input_bpl.o iotbx/pdb/xray_structure_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_geometry_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_geometry_ext.so.0 cctbx/geometry/boost_python/geometry_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_uctbx_ext.so.0.0.1' + 'lib/cctbx_uctbx_ext.so.0'->'lib/cctbx_uctbx_ext.so.0.0.1' + 'lib/cctbx_uctbx_ext.so'->'lib/cctbx_uctbx_ext.so.0.0.1' +g++ -o lib/cctbx_multipolar_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_multipolar_ext.so.0 cctbx/multipolar/aspherical_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_math_ext.so.0.0.1' + 'lib/cctbx_math_ext.so.0'->'lib/cctbx_math_ext.so.0.0.1' + 'lib/cctbx_math_ext.so'->'lib/cctbx_math_ext.so.0.0.1' +g++ -o lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_xray_scattering_ext.so.0 cctbx/eltbx/boost_python/xray_scattering_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15561,9 +15588,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.soCreate symlinks for: 'lib/gltbx_util_ext.so.0.0.1' - 'lib/gltbx_util_ext.so.0'->'lib/gltbx_util_ext.so.0.0.1' - 'lib/gltbx_util_ext.so'->'lib/gltbx_util_ext.so.0.0.1' +Create symlinks for: 'lib/cctbx_emma_ext.so.0.0.1' + 'lib/cctbx_emma_ext.so.0'->'lib/cctbx_emma_ext.so.0.0.1' + 'lib/cctbx_emma_ext.so'->'lib/cctbx_emma_ext.so.0.0.1' +g++ -o lib/cctbx_covariance_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_covariance_ext.so.0 cctbx/covariance/boost_python/covariance_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15572,7 +15600,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15580,7 +15608,15 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/cctbx_anharmonic_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_anharmonic_ext.so.0 cctbx/adptbx/boost_python/anharmonic_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_maptbx_bcr_bcr_ext.so.0 cctbx/maptbx/bcr/bcr_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_multipolar_ext.so.0.0.1' + 'lib/cctbx_multipolar_ext.so.0'->'lib/cctbx_multipolar_ext.so.0.0.1' + 'lib/cctbx_multipolar_ext.so'->'lib/cctbx_multipolar_ext.so.0.0.1' +g++ -o lib/cctbx_french_wilson_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_french_wilson_ext.so.0 cctbx/boost_python/french_wilson_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_covariance_ext.so.0.0.1' + 'lib/cctbx_covariance_ext.so.0'->'lib/cctbx_covariance_ext.so.0.0.1' + 'lib/cctbx_covariance_ext.so'->'lib/cctbx_covariance_ext.so.0.0.1' +g++ -o lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_attenuation_coefficient_ext.so.0 cctbx/eltbx/boost_python/attenuation_coefficient_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15589,28 +15625,20 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_anharmonic_ext.so.0.0.1' - 'lib/cctbx_anharmonic_ext.so.0'->'lib/cctbx_anharmonic_ext.so.0.0.1' - 'lib/cctbx_anharmonic_ext.so'->'lib/cctbx_anharmonic_ext.so.0.0.1' -g++ -o lib/gltbx_quadrics_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_quadrics_ext.so.0 gltbx/quadrics_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm -Create symlinks for: 'lib/cctbx_geometry_ext.so.0.0.1' - 'lib/cctbx_geometry_ext.so.0'->'lib/cctbx_geometry_ext.so.0.0.1' - 'lib/cctbx_geometry_ext.so'->'lib/cctbx_geometry_ext.so.0.0.1' -g++ -o lib/cctbx_eltbx_wavelengths_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_wavelengths_ext.so.0 cctbx/eltbx/boost_python/wavelengths_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_xray_ext.so.0.0.1' + 'lib/cctbx_xray_ext.so.0'->'lib/cctbx_xray_ext.so.0.0.1' + 'lib/cctbx_xray_ext.so'->'lib/cctbx_xray_ext.so.0.0.1' +Create symlinks for: 'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' + 'lib/cctbx_eltbx_xray_scattering_ext.so.0'->'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' + 'lib/cctbx_eltbx_xray_scattering_ext.so'->'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/iotbx_pdb_ext.so.0.0.1' - 'lib/iotbx_pdb_ext.so.0'->'lib/iotbx_pdb_ext.so.0.0.1' - 'lib/iotbx_pdb_ext.so'->'lib/iotbx_pdb_ext.so.0.0.1' -g++ -o lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_covalent_radii_ext.so.0 cctbx/eltbx/boost_python/covalent_radii_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15619,50 +15647,55 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/gltbx_quadrics_ext.so.0.0.1' - 'lib/gltbx_quadrics_ext.so.0'->'lib/gltbx_quadrics_ext.so.0.0.1' - 'lib/gltbx_quadrics_ext.so'->'lib/gltbx_quadrics_ext.so.0.0.1' -g++ -o lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_maptbx_bcr_bcr_ext.so.0 cctbx/maptbx/bcr/bcr_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1' - 'lib/cctbx_eltbx_wavelengths_ext.so.0'->'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1' - 'lib/cctbx_eltbx_wavelengths_ext.so'->'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1' +Create symlinks for: 'lib/dxtbx_model_ext.so.0.0.1' + 'lib/dxtbx_model_ext.so.0'->'lib/dxtbx_model_ext.so.0.0.1' + 'lib/dxtbx_model_ext.so'->'lib/dxtbx_model_ext.so.0.0.1' +Create symlinks for: 'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' + 'lib/cctbx_maptbx_bcr_bcr_ext.so.0'->'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' + 'lib/cctbx_maptbx_bcr_bcr_ext.so'->'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' g++ -o lib/dxtbx_masking_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_masking_ext.so.0 dxtbx/src/dxtbx/masking/boost_python/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python313 -lcbf -lhdf5 +Create symlinks for: 'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1' + 'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0'->'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1' + 'lib/cctbx_eltbx_attenuation_coefficient_ext.so'->'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1' +Create symlinks for: 'lib/cctbx_french_wilson_ext.so.0.0.1' + 'lib/cctbx_french_wilson_ext.so.0'->'lib/cctbx_french_wilson_ext.so.0.0.1' + 'lib/cctbx_french_wilson_ext.so'->'lib/cctbx_french_wilson_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/gltbx_fonts_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_fonts_ext.so.0 gltbx/fonts_ext.o gltbx/font_ucs_8x13.o gltbx/font_ucs_9x15.o gltbx/font_ucs_10x20.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm +g++ -o lib/cctbx_eltbx_sasaki_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_sasaki_ext.so.0 cctbx/eltbx/boost_python/sasaki_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_array_family_flex_ext.so.0 cctbx/array_family/boost_python/flex_ext.o cctbx/array_family/boost_python/flex_hendrickson_lattman.o cctbx/array_family/boost_python/flex_miller_index.o cctbx/array_family/boost_python/flex_xray_scatterer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_merging_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_merging_ext.so.0 cctbx/merging/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_miller_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_miller_ext.so.0 cctbx/miller/boost_python/miller_ext.o cctbx/miller/boost_python/asu.o cctbx/miller/boost_python/bins.o cctbx/miller/boost_python/change_basis.o cctbx/miller/boost_python/expand_to_p1.o cctbx/miller/boost_python/index_generator.o cctbx/miller/boost_python/index_span.o cctbx/miller/boost_python/match_bijvoet_mates.o cctbx/miller/boost_python/match_indices.o cctbx/miller/boost_python/match_multi_indices.o cctbx/miller/boost_python/merge_equivalents.o cctbx/miller/boost_python/phase_integrator.o cctbx/miller/boost_python/phase_transfer.o cctbx/miller/boost_python/sym_equiv.o cctbx/miller/boost_python/f_calc_map.o cctbx/miller/boost_python/lookup_utils.o cctbx/miller/boost_python/amplitude_normalisation.o cctbx/miller/boost_python/randomize_amplitude_and_phase.o cctbx/miller/boost_python/slices.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_masks_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_masks_ext.so.0 cctbx/masks/boost_python/masks_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' - 'lib/cctbx_maptbx_bcr_bcr_ext.so.0'->'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' - 'lib/cctbx_maptbx_bcr_bcr_ext.so'->'lib/cctbx_maptbx_bcr_bcr_ext.so.0.0.1' -g++ -o lib/cctbx_uctbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_uctbx_ext.so.0 cctbx/uctbx/boost_python/uctbx_ext.o cctbx/uctbx/boost_python/fast_minimum_reduction.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1' - 'lib/cctbx_eltbx_covalent_radii_ext.so.0'->'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1' - 'lib/cctbx_eltbx_covalent_radii_ext.so'->'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1' -g++ -o lib/cctbx_emma_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_emma_ext.so.0 cctbx/boost_python/emma_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libboost_thread.soCreate symlinks for: 'lib/cctbx_xray_ext.so.0.0.1' - 'lib/cctbx_xray_ext.so.0'->'lib/cctbx_xray_ext.so.0.0.1' - 'lib/cctbx_xray_ext.so'->'lib/cctbx_xray_ext.so.0.0.1' -: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/gltbx_fonts_ext.so.0.0.1' + 'lib/gltbx_fonts_ext.so.0'->'lib/gltbx_fonts_ext.so.0.0.1' + 'lib/gltbx_fonts_ext.so'->'lib/gltbx_fonts_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15671,6 +15704,11 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_icsd_radii_ext.so.0 cctbx/eltbx/boost_python/icsd_radii_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' + 'lib/cctbx_eltbx_sasaki_ext.so.0'->'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' + 'lib/cctbx_eltbx_sasaki_ext.so'->'lib/cctbx_eltbx_sasaki_ext.so.0.0.1' +g++ -o lib/dxtbx_flumpy.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_flumpy.so.0 dxtbx/src/dxtbx/boost_python/flumpy.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python313 -lcbf -lhdf5 /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15679,15 +15717,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_emma_ext.so.0.0.1' - 'lib/cctbx_emma_ext.so.0'->'lib/cctbx_emma_ext.so.0.0.1' - 'lib/cctbx_emma_ext.so'->'lib/cctbx_emma_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_uctbx_ext.so.0.0.1' - 'lib/cctbx_uctbx_ext.so.0'->'lib/cctbx_uctbx_ext.so.0.0.1' - 'lib/cctbx_uctbx_ext.so'->'lib/cctbx_uctbx_ext.so.0.0.1' -g++ -o lib/cctbx_eltbx_henke_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_henke_ext.so.0 cctbx/eltbx/boost_python/henke_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_covariance_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_covariance_ext.so.0 cctbx/covariance/boost_python/covariance_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_eltbx_neutron_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_neutron_ext.so.0 cctbx/eltbx/boost_python/neutron_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_merging_ext.so.0.0.1' + 'lib/cctbx_merging_ext.so.0'->'lib/cctbx_merging_ext.so.0.0.1' + 'lib/cctbx_merging_ext.so'->'lib/cctbx_merging_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15696,10 +15728,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_eltbx_henke_ext.so.0.0.1' - 'lib/cctbx_eltbx_henke_ext.so.0'->'lib/cctbx_eltbx_henke_ext.so.0.0.1' - 'lib/cctbx_eltbx_henke_ext.so'->'lib/cctbx_eltbx_henke_ext.so.0.0.1' -g++ -o lib/cctbx_multipolar_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_multipolar_ext.so.0 cctbx/multipolar/aspherical_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_asymmetric_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_asymmetric_map_ext.so.0 cctbx/maptbx/asymmetric_map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lasymmetric_map -liotbx_xplor -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/dxtbx_masking_ext.so.0.0.1' + 'lib/dxtbx_masking_ext.so.0'->'lib/dxtbx_masking_ext.so.0.0.1' + 'lib/dxtbx_masking_ext.so'->'lib/dxtbx_masking_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15716,33 +15748,27 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/cctbx_adptbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_adptbx_ext.so.0 cctbx/adptbx/boost_python/adptbx_ext.o cctbx/adptbx/boost_python/hirshfeld.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_masks_ext.so.0.0.1' + 'lib/cctbx_masks_ext.so.0'->'lib/cctbx_masks_ext.so.0.0.1' + 'lib/cctbx_masks_ext.so'->'lib/cctbx_masks_ext.so.0.0.1' +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/dxtbx_masking_ext.so.0.0.1' - 'lib/dxtbx_masking_ext.so.0'->'lib/dxtbx_masking_ext.so.0.0.1' - 'lib/dxtbx_masking_ext.so'->'lib/dxtbx_masking_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_multipolar_ext.so.0.0.1' - 'lib/cctbx_multipolar_ext.so.0'->'lib/cctbx_multipolar_ext.so.0.0.1' - 'lib/cctbx_multipolar_ext.so'->'lib/cctbx_multipolar_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_covariance_ext.so.0.0.1' - 'lib/cctbx_covariance_ext.so.0'->'lib/cctbx_covariance_ext.so.0.0.1' - 'lib/cctbx_covariance_ext.so'->'lib/cctbx_covariance_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_eltbx_neutron_ext.so.0.0.1' - 'lib/cctbx_eltbx_neutron_ext.so.0'->'lib/cctbx_eltbx_neutron_ext.so.0.0.1' - 'lib/cctbx_eltbx_neutron_ext.so'->'lib/cctbx_eltbx_neutron_ext.so.0.0.1' -g++ -o lib/cctbx_french_wilson_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_french_wilson_ext.so.0 cctbx/boost_python/french_wilson_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_sgtbx_asu_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_sgtbx_asu_ext.so.0 cctbx/sgtbx/direct_space_asu/proto/asu_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/dxtbx_flumpy.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_flumpy.so.0 dxtbx/src/dxtbx/boost_python/flumpy.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python313 -lcbf -lhdf5 -g++ -o lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_tiny_pse_ext.so.0 cctbx/eltbx/boost_python/tiny_pse_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/dxtbx_model_ext.so.0.0.1' - 'lib/dxtbx_model_ext.so.0'->'lib/dxtbx_model_ext.so.0.0.1' - 'lib/dxtbx_model_ext.so'->'lib/dxtbx_model_ext.so.0.0.1' +g++ -o lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_fp_fdp_ext.so.0 cctbx/eltbx/boost_python/fp_fdp_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1' + 'lib/cctbx_eltbx_icsd_radii_ext.so.0'->'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1' + 'lib/cctbx_eltbx_icsd_radii_ext.so'->'lib/cctbx_eltbx_icsd_radii_ext.so.0.0.1' +g++ -o lib/cctbx_maptbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_maptbx_ext.so.0 cctbx/maptbx/boost_python/maptbx_ext.o cctbx/maptbx/boost_python/grid_indices_around_sites.o cctbx/maptbx/boost_python/grid_tags.o cctbx/maptbx/boost_python/gridding.o cctbx/maptbx/boost_python/misc.o cctbx/maptbx/boost_python/peak_search.o cctbx/maptbx/boost_python/pymol_interface.o cctbx/maptbx/boost_python/statistics.o cctbx/maptbx/boost_python/structure_factors.o cctbx/maptbx/boost_python/coordinate_transformers.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15767,34 +15793,36 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1' + 'lib/cctbx_eltbx_fp_fdp_ext.so.0'->'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1' + 'lib/cctbx_eltbx_fp_fdp_ext.so'->'lib/cctbx_eltbx_fp_fdp_ext.so.0.0.1' +g++ -o lib/gltbx_util_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_util_ext.so.0 gltbx/util_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm +Create symlinks for: 'lib/dxtbx_flumpy.so.0.0.1' + 'lib/dxtbx_flumpy.so.0'->'lib/dxtbx_flumpy.so.0.0.1' + 'lib/dxtbx_flumpy.so'->'lib/dxtbx_flumpy.so.0.0.1' +Create symlinks for: 'lib/cctbx_asymmetric_map_ext.so.0.0.1' + 'lib/cctbx_asymmetric_map_ext.so.0'->'lib/cctbx_asymmetric_map_ext.so.0.0.1' + 'lib/cctbx_asymmetric_map_ext.so'->'lib/cctbx_asymmetric_map_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_french_wilson_ext.so.0.0.1' - 'lib/cctbx_french_wilson_ext.so.0'->'lib/cctbx_french_wilson_ext.so.0.0.1' - 'lib/cctbx_french_wilson_ext.so'->'lib/cctbx_french_wilson_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1' - 'lib/cctbx_eltbx_tiny_pse_ext.so.0'->'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1' - 'lib/cctbx_eltbx_tiny_pse_ext.so'->'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1' -g++ -o lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_chemical_elements_ext.so.0 cctbx/eltbx/boost_python/chemical_elements_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_merging_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_merging_ext.so.0 cctbx/merging/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_masks_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_masks_ext.so.0 cctbx/masks/boost_python/masks_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_miller_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_miller_ext.so.0 cctbx/miller/boost_python/miller_ext.o cctbx/miller/boost_python/asu.o cctbx/miller/boost_python/bins.o cctbx/miller/boost_python/change_basis.o cctbx/miller/boost_python/expand_to_p1.o cctbx/miller/boost_python/index_generator.o cctbx/miller/boost_python/index_span.o cctbx/miller/boost_python/match_bijvoet_mates.o cctbx/miller/boost_python/match_indices.o cctbx/miller/boost_python/match_multi_indices.o cctbx/miller/boost_python/merge_equivalents.o cctbx/miller/boost_python/phase_integrator.o cctbx/miller/boost_python/phase_transfer.o cctbx/miller/boost_python/sym_equiv.o cctbx/miller/boost_python/f_calc_map.o cctbx/miller/boost_python/lookup_utils.o cctbx/miller/boost_python/amplitude_normalisation.o cctbx/miller/boost_python/randomize_amplitude_and_phase.o cctbx/miller/boost_python/slices.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/cctbx_sgtbx_ext.so.0.0.1' - 'lib/cctbx_sgtbx_ext.so.0'->'lib/cctbx_sgtbx_ext.so.0.0.1' - 'lib/cctbx_sgtbx_ext.so'->'lib/cctbx_sgtbx_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_sgtbx_asu_ext.so.0.0.1' - 'lib/cctbx_sgtbx_asu_ext.so.0'->'lib/cctbx_sgtbx_asu_ext.so.0.0.1' - 'lib/cctbx_sgtbx_asu_ext.so'->'lib/cctbx_sgtbx_asu_ext.so.0.0.1' +g++ -o lib/cctbx_geometry_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_geometry_restraints_ext.so.0 cctbx/geometry_restraints/geometry_restraints_ext.o cctbx/geometry_restraints/bond_bpl.o cctbx/geometry_restraints/bond_similarity_bpl.o cctbx/geometry_restraints/bond_sorted_bpl.o cctbx/geometry_restraints/nonbonded_bpl.o cctbx/geometry_restraints/nonbonded_sorted_bpl.o cctbx/geometry_restraints/angle_bpl.o cctbx/geometry_restraints/dihedral_bpl.o cctbx/geometry_restraints/chirality_bpl.o cctbx/geometry_restraints/planarity_bpl.o cctbx/geometry_restraints/parallelity_bpl.o cctbx/geometry_restraints/motif_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/gltbx_quadrics_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_quadrics_ext.so.0 gltbx/quadrics_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm +Create symlinks for: 'lib/cctbx_adptbx_ext.so.0.0.1' + 'lib/cctbx_adptbx_ext.so.0'->'lib/cctbx_adptbx_ext.so.0.0.1' + 'lib/cctbx_adptbx_ext.so'->'lib/cctbx_adptbx_ext.so.0.0.1' +Create symlinks for: 'lib/gltbx_util_ext.so.0.0.1' + 'lib/gltbx_util_ext.so.0'->'lib/gltbx_util_ext.so.0.0.1' + 'lib/gltbx_util_ext.so'->'lib/gltbx_util_ext.so.0.0.1' +g++ -o lib/cctbx_xray_observations_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_xray_observations_ext.so.0 cctbx/xray/observations/boost_python/observations.o cctbx/xray/observations/boost_python/observations_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_crystal_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_crystal_ext.so.0 cctbx/crystal/crystal_ext.o cctbx/crystal/asu_clusters_bpl.o cctbx/crystal/close_packing_bpl.o cctbx/crystal/coordination_sequences_bpl.o cctbx/crystal/direct_space_asu_bpl.o cctbx/crystal/incremental_pairs_bpl.o cctbx/crystal/neighbors_bpl.o cctbx/crystal/pair_tables_bpl.o cctbx/crystal/site_cluster_analysis_bpl.o cctbx/crystal/symmetry_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15803,17 +15831,20 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.soCreate symlinks for: 'lib/dxtbx_flumpy.so.0.0.1' - 'lib/dxtbx_flumpy.so.0'->'lib/dxtbx_flumpy.so.0.0.1' - 'lib/dxtbx_flumpy.so'->'lib/dxtbx_flumpy.so.0.0.1' -: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/cctbx_array_family_flex_ext.so.0.0.1' + 'lib/cctbx_array_family_flex_ext.so.0'->'lib/cctbx_array_family_flex_ext.so.0.0.1' + 'lib/cctbx_array_family_flex_ext.so'->'lib/cctbx_array_family_flex_ext.so.0.0.1' +g++ -o lib/dxtbx_imageset_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_imageset_ext.so.0 dxtbx/src/dxtbx/boost_python/imageset_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lhdf5 -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python313 -lcbf -lhdf5 /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15822,39 +15853,43 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1' - 'lib/cctbx_eltbx_chemical_elements_ext.so.0'->'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1' - 'lib/cctbx_eltbx_chemical_elements_ext.so'->'lib/cctbx_eltbx_chemical_elements_ext.so.0.0.1' -g++ -o lib/gltbx_glu_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_glu_ext.so.0 gltbx/glu_ext.o gltbx/glu_defines_00_bpl.o gltbx/glu_defines_01_bpl.o gltbx/glu_functions_00_bpl.o gltbx/glu_functions_01_bpl.o gltbx/glu_functions_02_bpl.o gltbx/glu_functions_03_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm -Create symlinks for: 'lib/cctbx_masks_ext.so.0.0.1' - 'lib/cctbx_masks_ext.so.0'->'lib/cctbx_masks_ext.so.0.0.1' - 'lib/cctbx_masks_ext.so'->'lib/cctbx_masks_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_merging_ext.so.0.0.1' - 'lib/cctbx_merging_ext.so.0'->'lib/cctbx_merging_ext.so.0.0.1' - 'lib/cctbx_merging_ext.so'->'lib/cctbx_merging_ext.so.0.0.1' +Create symlinks for: 'lib/gltbx_quadrics_ext.so.0.0.1' + 'lib/gltbx_quadrics_ext.so.0'->'lib/gltbx_quadrics_ext.so.0.0.1' + 'lib/gltbx_quadrics_ext.so'->'lib/gltbx_quadrics_ext.so.0.0.1' +g++ -o lib/cctbx_statistics_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_statistics_ext.so.0 cctbx/boost_python/statistics_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/cctbx_adptbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_adptbx_ext.so.0 cctbx/adptbx/boost_python/adptbx_ext.o cctbx/adptbx/boost_python/hirshfeld.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/gltbx_viewer_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_viewer_utils_ext.so.0 gltbx/viewer_utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm -g++ -o lib/cctbx_asymmetric_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_asymmetric_map_ext.so.0 cctbx/maptbx/asymmetric_map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lasymmetric_map -liotbx_xplor -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/cctbx_maptbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_maptbx_ext.so.0 cctbx/maptbx/boost_python/maptbx_ext.o cctbx/maptbx/boost_python/grid_indices_around_sites.o cctbx/maptbx/boost_python/grid_tags.o cctbx/maptbx/boost_python/gridding.o cctbx/maptbx/boost_python/misc.o cctbx/maptbx/boost_python/peak_search.o cctbx/maptbx/boost_python/pymol_interface.o cctbx/maptbx/boost_python/statistics.o cctbx/maptbx/boost_python/structure_factors.o cctbx/maptbx/boost_python/coordinate_transformers.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/gltbx_gl_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=gltbx_gl_ext.so.0 gltbx/gl_ext.o gltbx/gl_defines_00_bpl.o gltbx/gl_defines_01_bpl.o gltbx/gl_defines_02_bpl.o gltbx/gl_defines_03_bpl.o gltbx/gl_defines_04_bpl.o gltbx/gl_defines_05_bpl.o gltbx/gl_defines_06_bpl.o gltbx/gl_defines_07_bpl.o gltbx/gl_functions_00_bpl.o gltbx/gl_functions_01_bpl.o gltbx/gl_functions_02_bpl.o gltbx/gl_functions_03_bpl.o gltbx/gl_functions_04_bpl.o gltbx/gl_functions_05_bpl.o gltbx/gl_functions_06_bpl.o gltbx/gl_functions_07_bpl.o gltbx/gl_functions_08_bpl.o gltbx/gl_functions_09_bpl.o gltbx/gl_functions_10_bpl.o gltbx/gl_functions_11_bpl.o gltbx/gl_functions_12_bpl.o gltbx/gl_functions_13_bpl.o gltbx/gl_functions_14_bpl.o gltbx/gl_functions_15_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lGLU -lGL -lm +Create symlinks for: 'lib/cctbx_xray_observations_ext.so.0.0.1' + 'lib/cctbx_xray_observations_ext.so.0'->'lib/cctbx_xray_observations_ext.so.0.0.1' + 'lib/cctbx_xray_observations_ext.so'->'lib/cctbx_xray_observations_ext.so.0.0.1' +g++ -o lib/cctbx_sgtbx_asu_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_sgtbx_asu_ext.so.0 cctbx/sgtbx/direct_space_asu/proto/asu_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx_sgtbx_asu -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/cctbx_statistics_ext.so.0.0.1' + 'lib/cctbx_statistics_ext.so.0'->'lib/cctbx_statistics_ext.so.0.0.1' + 'lib/cctbx_statistics_ext.so'->'lib/cctbx_statistics_ext.so.0.0.1' +g++ -o lib/iotbx_mtz_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_mtz_ext.so.0 iotbx/mtz/ext.o iotbx/mtz/object_bpl.o iotbx/mtz/crystal_bpl.o iotbx/mtz/dataset_bpl.o iotbx/mtz/column_bpl.o iotbx/mtz/batch_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_mtz -lcctbx -lccp4io -lccp4c -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_orientation_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_orientation_ext.so.0 cctbx/boost_python/orientation_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_miller_ext.so.0.0.1' + 'lib/cctbx_miller_ext.so.0'->'lib/cctbx_miller_ext.so.0.0.1' + 'lib/cctbx_miller_ext.so'->'lib/cctbx_miller_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15871,46 +15906,30 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/gltbx_glu_ext.so.0.0.1' - 'lib/gltbx_glu_ext.so.0'->'lib/gltbx_glu_ext.so.0.0.1' - 'lib/gltbx_glu_ext.so'->'lib/gltbx_glu_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/dxtbx_imageset_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=dxtbx_imageset_ext.so.0 dxtbx/src/dxtbx/boost_python/imageset_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/base/lib -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lm -ltiff -lboost_python313 -lcbf -lhdf5 -lboost_thread -lboost_system -lm -lcctbx -lscitbx_boost_python -ltiff -lboost_python313 -lcbf -lhdf5 /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGLU.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libGL.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_asymmetric_map_ext.so.0.0.1' - 'lib/cctbx_asymmetric_map_ext.so.0'->'lib/cctbx_asymmetric_map_ext.so.0.0.1' - 'lib/cctbx_asymmetric_map_ext.so'->'lib/cctbx_asymmetric_map_ext.so.0.0.1' -g++ -o lib/cctbx_geometry_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_geometry_restraints_ext.so.0 cctbx/geometry_restraints/geometry_restraints_ext.o cctbx/geometry_restraints/bond_bpl.o cctbx/geometry_restraints/bond_similarity_bpl.o cctbx/geometry_restraints/bond_sorted_bpl.o cctbx/geometry_restraints/nonbonded_bpl.o cctbx/geometry_restraints/nonbonded_sorted_bpl.o cctbx/geometry_restraints/angle_bpl.o cctbx/geometry_restraints/dihedral_bpl.o cctbx/geometry_restraints/chirality_bpl.o cctbx/geometry_restraints/planarity_bpl.o cctbx/geometry_restraints/parallelity_bpl.o cctbx/geometry_restraints/motif_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/gltbx_viewer_utils_ext.so.0.0.1' - 'lib/gltbx_viewer_utils_ext.so.0'->'lib/gltbx_viewer_utils_ext.so.0.0.1' - 'lib/gltbx_viewer_utils_ext.so'->'lib/gltbx_viewer_utils_ext.so.0.0.1' -g++ -o lib/cctbx_math_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_math_ext.so.0 cctbx/math/boost_python/math_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/cctbx_eltbx_wavelengths_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_wavelengths_ext.so.0 cctbx/eltbx/boost_python/wavelengths_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_orientation_ext.so.0.0.1' + 'lib/cctbx_orientation_ext.so.0'->'lib/cctbx_orientation_ext.so.0.0.1' + 'lib/cctbx_orientation_ext.so'->'lib/cctbx_orientation_ext.so.0.0.1' +g++ -o lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_covalent_radii_ext.so.0 cctbx/eltbx/boost_python/covalent_radii_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15932,18 +15951,22 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_adptbx_ext.so.0.0.1' - 'lib/cctbx_adptbx_ext.so.0'->'lib/cctbx_adptbx_ext.so.0.0.1' - 'lib/cctbx_adptbx_ext.so'->'lib/cctbx_adptbx_ext.so.0.0.1' -g++ -o lib/iotbx_mtz_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_mtz_ext.so.0 iotbx/mtz/ext.o iotbx/mtz/object_bpl.o iotbx/mtz/crystal_bpl.o iotbx/mtz/dataset_bpl.o iotbx/mtz/column_bpl.o iotbx/mtz/batch_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_mtz -lcctbx -lccp4io -lccp4c -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/cctbx_math_ext.so.0.0.1' - 'lib/cctbx_math_ext.so.0'->'lib/cctbx_math_ext.so.0.0.1' - 'lib/cctbx_math_ext.so'->'lib/cctbx_math_ext.so.0.0.1' -g++ -o lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_xray_scattering_ext.so.0 cctbx/eltbx/boost_python/xray_scattering_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/gltbx_gl_ext.so.0.0.1' - 'lib/gltbx_gl_ext.so.0'->'lib/gltbx_gl_ext.so.0.0.1' - 'lib/gltbx_gl_ext.so'->'lib/gltbx_gl_ext.so.0.0.1' -g++ -o lib/cctbx_xray_observations_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_xray_observations_ext.so.0 cctbx/xray/observations/boost_python/observations.o cctbx/xray/observations/boost_python/observations_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_sgtbx_asu_ext.so.0.0.1' + 'lib/cctbx_sgtbx_asu_ext.so.0'->'lib/cctbx_sgtbx_asu_ext.so.0.0.1' + 'lib/cctbx_sgtbx_asu_ext.so'->'lib/cctbx_sgtbx_asu_ext.so.0.0.1' +g++ -o lib/cctbx_adp_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_adp_restraints_ext.so.0 cctbx/adp_restraints/adp_restraints_bpl.o cctbx/adp_restraints/adp_restraints_ext.o cctbx/adp_restraints/rigid_bond_bpl.o cctbx/adp_restraints/rigu_bpl.o cctbx/adp_restraints/adp_similarity_bpl.o cctbx/adp_restraints/isotropic_adp_bpl.o cctbx/adp_restraints/aniso_restraints_bpl.o cctbx/adp_restraints/fixed_u_eq_adp_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1' + 'lib/cctbx_eltbx_covalent_radii_ext.so.0'->'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1' + 'lib/cctbx_eltbx_covalent_radii_ext.so'->'lib/cctbx_eltbx_covalent_radii_ext.so.0.0.1' +g++ -o lib/cctbx_translation_search_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_translation_search_ext.so.0 cctbx/translation_search/boost_python/translation_search_ext.o cctbx/translation_search/boost_python/fast_nv1995.o cctbx/translation_search/boost_python/fast_terms.o cctbx/translation_search/boost_python/symmetry_flags.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1' + 'lib/cctbx_eltbx_wavelengths_ext.so.0'->'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1' + 'lib/cctbx_eltbx_wavelengths_ext.so'->'lib/cctbx_eltbx_wavelengths_ext.so.0.0.1' +g++ -o lib/determine_unit_cell_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=determine_unit_cell_ext.so.0 cctbx/uctbx/determine_unit_cell/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_eltbx_neutron_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_neutron_ext.so.0 cctbx/eltbx/boost_python/neutron_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_maptbx_ext.so.0.0.1' + 'lib/cctbx_maptbx_ext.so.0'->'lib/cctbx_maptbx_ext.so.0.0.1' + 'lib/cctbx_maptbx_ext.so'->'lib/cctbx_maptbx_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15960,6 +15983,13 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/cctbx_dmtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_dmtbx_ext.so.0 cctbx/dmtbx/boost_python/dmtbx_ext.o cctbx/dmtbx/boost_python/triplet_phase_relation.o cctbx/dmtbx/boost_python/triplet_generator.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/dxtbx_imageset_ext.so.0.0.1' + 'lib/dxtbx_imageset_ext.so.0'->'lib/dxtbx_imageset_ext.so.0.0.1' + 'lib/dxtbx_imageset_ext.so'->'lib/dxtbx_imageset_ext.so.0.0.1' +Create symlinks for: 'lib/determine_unit_cell_ext.so.0.0.1' + 'lib/determine_unit_cell_ext.so.0'->'lib/determine_unit_cell_ext.so.0.0.1' + 'lib/determine_unit_cell_ext.so'->'lib/determine_unit_cell_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15968,7 +15998,11 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/cctbx_crystal_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_crystal_ext.so.0 cctbx/crystal/crystal_ext.o cctbx/crystal/asu_clusters_bpl.o cctbx/crystal/close_packing_bpl.o cctbx/crystal/coordination_sequences_bpl.o cctbx/crystal/direct_space_asu_bpl.o cctbx/crystal/incremental_pairs_bpl.o cctbx/crystal/neighbors_bpl.o cctbx/crystal/pair_tables_bpl.o cctbx/crystal/site_cluster_analysis_bpl.o cctbx/crystal/symmetry_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_sgtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_sgtbx_ext.so.0 cctbx/sgtbx/boost_python/sgtbx_ext.o cctbx/sgtbx/boost_python/brick.o cctbx/sgtbx/boost_python/change_of_basis.o cctbx/sgtbx/boost_python/find_affine.o cctbx/sgtbx/boost_python/lattice_symmetry.o cctbx/sgtbx/boost_python/phase_info.o cctbx/sgtbx/boost_python/reciprocal_space_asu.o cctbx/sgtbx/boost_python/rot_mx.o cctbx/sgtbx/boost_python/rt_mx.o cctbx/sgtbx/boost_python/search_symmetry.o cctbx/sgtbx/boost_python/seminvariant.o cctbx/sgtbx/boost_python/site_symmetry.o cctbx/sgtbx/boost_python/space_group.o cctbx/sgtbx/boost_python/space_group_type.o cctbx/sgtbx/boost_python/sym_equiv_sites.o cctbx/sgtbx/boost_python/symbols.o cctbx/sgtbx/boost_python/tensor_rank_2.o cctbx/sgtbx/boost_python/tensors.o cctbx/sgtbx/boost_python/tr_vec.o cctbx/sgtbx/boost_python/wyckoff.o cctbx/sgtbx/boost_python/select_generators.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_tiny_pse_ext.so.0 cctbx/eltbx/boost_python/tiny_pse_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/cctbx_translation_search_ext.so.0.0.1' + 'lib/cctbx_translation_search_ext.so.0'->'lib/cctbx_translation_search_ext.so.0.0.1' + 'lib/cctbx_translation_search_ext.so'->'lib/cctbx_translation_search_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -15977,21 +16011,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/dxtbx_imageset_ext.so.0.0.1' - 'lib/dxtbx_imageset_ext.so.0'->'lib/dxtbx_imageset_ext.so.0.0.1' - 'lib/dxtbx_imageset_ext.so'->'lib/dxtbx_imageset_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' - 'lib/cctbx_eltbx_xray_scattering_ext.so.0'->'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' - 'lib/cctbx_eltbx_xray_scattering_ext.so'->'lib/cctbx_eltbx_xray_scattering_ext.so.0.0.1' -g++ -o lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=cctbx_eltbx_attenuation_coefficient_ext.so.0 cctbx/eltbx/boost_python/attenuation_coefficient_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o spotfinder/core_toolbox/spotfilter.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Ispotfinder/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/src -Ispotfinder/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/spotfilter.cpp -Create symlinks for: 'lib/cctbx_miller_ext.so.0.0.1' - 'lib/cctbx_miller_ext.so.0'->'lib/cctbx_miller_ext.so.0.0.1' - 'lib/cctbx_miller_ext.so'->'lib/cctbx_miller_ext.so.0.0.1' -Create symlinks for: 'lib/cctbx_xray_observations_ext.so.0.0.1' - 'lib/cctbx_xray_observations_ext.so.0'->'lib/cctbx_xray_observations_ext.so.0.0.1' - 'lib/cctbx_xray_observations_ext.so'->'lib/cctbx_xray_observations_ext.so.0.0.1' -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/iotbx_mtz_ext.so.0.0.1' + 'lib/iotbx_mtz_ext.so.0'->'lib/iotbx_mtz_ext.so.0.0.1' + 'lib/iotbx_mtz_ext.so'->'lib/iotbx_mtz_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16000,15 +16022,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1' - 'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0'->'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1' - 'lib/cctbx_eltbx_attenuation_coefficient_ext.so'->'lib/cctbx_eltbx_attenuation_coefficient_ext.so.0.0.1' -g++ -o mmtbx/masks/atom_mask.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/masks/atom_mask.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/iotbx_mtz_ext.so.0.0.1' - 'lib/iotbx_mtz_ext.so.0'->'lib/iotbx_mtz_ext.so.0.0.1' - 'lib/iotbx_mtz_ext.so'->'lib/iotbx_mtz_ext.so.0.0.1' -g++ -o mmtbx/tls/decompose.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/decompose.cpp +Create symlinks for: 'lib/cctbx_eltbx_neutron_ext.so.0.0.1' + 'lib/cctbx_eltbx_neutron_ext.so.0'->'lib/cctbx_eltbx_neutron_ext.so.0.0.1' + 'lib/cctbx_eltbx_neutron_ext.so'->'lib/cctbx_eltbx_neutron_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16017,34 +16033,76 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o mmtbx/masks/atom_mask.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/masks/atom_mask.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1' + 'lib/cctbx_eltbx_tiny_pse_ext.so.0'->'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1' + 'lib/cctbx_eltbx_tiny_pse_ext.so'->'lib/cctbx_eltbx_tiny_pse_ext.so.0.0.1' +g++ -o mmtbx/tls/decompose.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/decompose.cpp +Create symlinks for: 'lib/cctbx_dmtbx_ext.so.0.0.1' + 'lib/cctbx_dmtbx_ext.so.0'->'lib/cctbx_dmtbx_ext.so.0.0.1' + 'lib/cctbx_dmtbx_ext.so'->'lib/cctbx_dmtbx_ext.so.0.0.1' cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o rstbx/dps_core/dps_core.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/dps_core/dps_core.cpp -g++ -o rstbx/dps_core/directional_fft.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/dps_core/directional_fft.cpp +Create symlinks for: 'lib/cctbx_crystal_ext.so.0.0.1' + 'lib/cctbx_crystal_ext.so.0'->'lib/cctbx_crystal_ext.so.0.0.1' + 'lib/cctbx_crystal_ext.so'->'lib/cctbx_crystal_ext.so.0.0.1' cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o rstbx/dps_core/directional_fft.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/dps_core/directional_fft.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/cctbx_maptbx_ext.so.0.0.1' - 'lib/cctbx_maptbx_ext.so.0'->'lib/cctbx_maptbx_ext.so.0.0.1' - 'lib/cctbx_maptbx_ext.so'->'lib/cctbx_maptbx_ext.so.0.0.1' g++ -o rstbx/dps_core/direction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/dps_core/direction.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o rstbx/indexing_api/indexing_api.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/indexing_api/indexing_api.cpp +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/cctbx_crystal_ext.so.0.0.1' - 'lib/cctbx_crystal_ext.so.0'->'lib/cctbx_crystal_ext.so.0.0.1' - 'lib/cctbx_crystal_ext.so'->'lib/cctbx_crystal_ext.so.0.0.1' +Create symlinks for: 'lib/cctbx_adp_restraints_ext.so.0.0.1' + 'lib/cctbx_adp_restraints_ext.so.0'->'lib/cctbx_adp_restraints_ext.so.0.0.1' + 'lib/cctbx_adp_restraints_ext.so'->'lib/cctbx_adp_restraints_ext.so.0.0.1' g++ -o rstbx/diffraction/ewald_sphere.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/diffraction/ewald_sphere.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/libspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libspotfinder.so.0 spotfinder/core_toolbox/spot.o spotfinder/core_toolbox/libdistl.o spotfinder/core_toolbox/hough.o spotfinder/core_toolbox/distl.o spotfinder/core_toolbox/spotfilter.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lann-cctbx -lomptbx -lm +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/cctbx_geometry_restraints_ext.so.0.0.1' + 'lib/cctbx_geometry_restraints_ext.so.0'->'lib/cctbx_geometry_restraints_ext.so.0.0.1' + 'lib/cctbx_geometry_restraints_ext.so'->'lib/cctbx_geometry_restraints_ext.so.0.0.1' +Create symlinks for: 'lib/libspotfinder.so.0.0.1' + 'lib/libspotfinder.so.0'->'lib/libspotfinder.so.0.0.1' + 'lib/libspotfinder.so'->'lib/libspotfinder.so.0.0.1' g++ -o rstbx/diffraction/partial_spot_position_partial_H.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/diffraction/partial_spot_position_partial_H.cpp -g++ -o scitbx/minpack/raw.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/minpack/raw.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/libdxtbxspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libdxtbxspotfinder.so.0 spotfinder/dxtbx_toolbox/libdistl.o spotfinder/dxtbx_toolbox/distl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lspotfinder -lann-cctbx -lomptbx -lm +Create symlinks for: 'lib/cctbx_sgtbx_ext.so.0.0.1' + 'lib/cctbx_sgtbx_ext.so.0'->'lib/cctbx_sgtbx_ext.so.0.0.1' + 'lib/cctbx_sgtbx_ext.so'->'lib/cctbx_sgtbx_ext.so.0.0.1' +/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/libdxtbxspotfinder.so.0.0.1' + 'lib/libdxtbxspotfinder.so.0'->'lib/libdxtbxspotfinder.so.0.0.1' + 'lib/libdxtbxspotfinder.so'->'lib/libdxtbxspotfinder.so.0.0.1' +g++ -o scitbx/minpack/raw.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/minpack/raw.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ gcc -o scitbx/slatec/lib_c.o -c -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/slatec/lib_c.c -Create symlinks for: 'lib/cctbx_geometry_restraints_ext.so.0.0.1' - 'lib/cctbx_geometry_restraints_ext.so.0'->'lib/cctbx_geometry_restraints_ext.so.0.0.1' - 'lib/cctbx_geometry_restraints_ext.so'->'lib/cctbx_geometry_restraints_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/affine.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/affine.cpp -g++ -o lib/libscitbx_slatec.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libscitbx_slatec.so.0 scitbx/slatec/lib_c.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lm cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/libscitbx_slatec.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libscitbx_slatec.so.0 scitbx/slatec/lib_c.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lm /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16058,53 +16116,31 @@ 'lib/libscitbx_slatec.so'->'lib/libscitbx_slatec.so.0.0.1' g++ -o smtbx/refinement/constraints/geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/geometrical_hydrogens.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/libscitbx_minpack.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libscitbx_minpack.so.0 scitbx/minpack/raw.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lm g++ -o smtbx/refinement/constraints/occupancy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/occupancy.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/libscitbx_minpack.so.0.0.1' - 'lib/libscitbx_minpack.so.0'->'lib/libscitbx_minpack.so.0.0.1' - 'lib/libscitbx_minpack.so'->'lib/libscitbx_minpack.so.0.0.1' g++ -o smtbx/refinement/constraints/reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/reparametrisation.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/refinement/constraints/rigid.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/rigid.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/libspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libspotfinder.so.0 spotfinder/core_toolbox/spot.o spotfinder/core_toolbox/libdistl.o spotfinder/core_toolbox/hough.o spotfinder/core_toolbox/distl.o spotfinder/core_toolbox/spotfilter.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lann-cctbx -lomptbx -lm -/usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. g++ -o smtbx/refinement/constraints/same_group.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/same_group.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/libspotfinder.so.0.0.1' - 'lib/libspotfinder.so.0'->'lib/libspotfinder.so.0.0.1' - 'lib/libspotfinder.so'->'lib/libspotfinder.so.0.0.1' -g++ -o lib/libdxtbxspotfinder.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libdxtbxspotfinder.so.0 spotfinder/dxtbx_toolbox/libdistl.o spotfinder/dxtbx_toolbox/distl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lspotfinder -lann-cctbx -lomptbx -lm -g++ -o smtbx/refinement/constraints/scaled_adp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/scaled_adp.cpp +g++ -o lib/libscitbx_minpack.so.0.0.1 -shared -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -Wl,-soname=libscitbx_minpack.so.0 scitbx/minpack/raw.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lm cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/libdxtbxspotfinder.so.0.0.1' - 'lib/libdxtbxspotfinder.so.0'->'lib/libdxtbxspotfinder.so.0.0.1' - 'lib/libdxtbxspotfinder.so'->'lib/libdxtbxspotfinder.so.0.0.1' +g++ -o smtbx/refinement/constraints/scaled_adp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/scaled_adp.cpp +g++ -o lib/libmmtbx_tls.so.0.0.1 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread -shared -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -Wl,-soname=libmmtbx_tls.so.0 mmtbx/tls/decompose.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lm +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/libscitbx_minpack.so.0.0.1' + 'lib/libscitbx_minpack.so.0'->'lib/libscitbx_minpack.so.0.0.1' + 'lib/libscitbx_minpack.so'->'lib/libscitbx_minpack.so.0.0.1' g++ -o smtbx/refinement/constraints/shared.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/shared.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/libmmtbx_tls.so.0.0.1 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread -shared -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -Wl,-soname=libmmtbx_tls.so.0 mmtbx/tls/decompose.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lm /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16172,6 +16208,7 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o mmtbx/geometry/boost_python/indexing_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/indexing_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/iotbx_pdb_hierarchy_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_pdb_hierarchy_ext.so.0 iotbx/pdb/hierarchy_ext.o iotbx/pdb/hierarchy_atom_bpl.o iotbx/pdb/hierarchy_atoms_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/wyckoff.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/direct_space_asu.h:4, @@ -16183,6 +16220,15 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ @@ -16204,6 +16250,19 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/mmtbx_dssp_ext.so.0.0.1' + 'lib/mmtbx_dssp_ext.so.0'->'lib/mmtbx_dssp_ext.so.0.0.1' + 'lib/mmtbx_dssp_ext.so'->'lib/mmtbx_dssp_ext.so.0.0.1' +g++ -o mmtbx/geometry/boost_python/primitive_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/primitive_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_array.hpp:23, from /usr/include/boost/shared_array.hpp:17, @@ -16230,20 +16289,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -g++ -o lib/mmtbx_dssp_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_dssp_ext.so.0 mmtbx/secondary_structure/dssp_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/iotbx_pdb_hierarchy_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=iotbx_pdb_hierarchy_ext.so.0 iotbx/pdb/hierarchy_ext.o iotbx/pdb/hierarchy_atom_bpl.o iotbx/pdb/hierarchy_atoms_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/mmtbx_dssp_ext.so.0.0.1' - 'lib/mmtbx_dssp_ext.so.0'->'lib/mmtbx_dssp_ext.so.0.0.1' - 'lib/mmtbx_dssp_ext.so'->'lib/mmtbx_dssp_ext.so.0.0.1' -g++ -o mmtbx/geometry/boost_python/primitive_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/primitive_ext.cpp +Create symlinks for: 'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' + 'lib/iotbx_pdb_hierarchy_ext.so.0'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' + 'lib/iotbx_pdb_hierarchy_ext.so'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' +g++ -o mmtbx/geometry/boost_python/shared_types_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/shared_types_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_alignment_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_alignment_ext.so.0 mmtbx/alignment/alignment_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16254,22 +16303,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. Create symlinks for: 'lib/mmtbx_alignment_ext.so.0.0.1' 'lib/mmtbx_alignment_ext.so.0'->'lib/mmtbx_alignment_ext.so.0.0.1' 'lib/mmtbx_alignment_ext.so'->'lib/mmtbx_alignment_ext.so.0.0.1' -g++ -o mmtbx/geometry/boost_python/shared_types_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/shared_types_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' - 'lib/iotbx_pdb_hierarchy_ext.so.0'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' - 'lib/iotbx_pdb_hierarchy_ext.so'->'lib/iotbx_pdb_hierarchy_ext.so.0.0.1' g++ -o mmtbx/geometry/boost_python/sphere_surface_sampling_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/sphere_surface_sampling_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_dynamics_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_dynamics_ext.so.0 mmtbx/dynamics/dynamics_ext.o mmtbx/dynamics/dynamics.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm @@ -16286,18 +16322,16 @@ 'lib/mmtbx_dynamics_ext.so.0'->'lib/mmtbx_dynamics_ext.so.0.0.1' 'lib/mmtbx_dynamics_ext.so'->'lib/mmtbx_dynamics_ext.so.0.0.1' g++ -o mmtbx/hydrogens/hydrogens_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/hydrogens/hydrogens_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/libmmtbx_masks.so.0.0.1' 'lib/libmmtbx_masks.so.0'->'lib/libmmtbx_masks.so.0.0.1' 'lib/libmmtbx_masks.so'->'lib/libmmtbx_masks.so.0.0.1' -g++ -o mmtbx/masks/masks_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/masks/masks_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, from /usr/include/boost/function/detail/prologue.hpp:12, from /usr/include/boost/function/function_template.hpp:13, @@ -16311,10 +16345,12 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/asa_ext.cpp:2: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/clash_ext.cpp:2: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +g++ -o mmtbx/masks/masks_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/masks/masks_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, from /usr/include/boost/function/detail/prologue.hpp:12, from /usr/include/boost/function/function_template.hpp:13, @@ -16322,25 +16358,12 @@ from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/converter/arg_to_python_base.hpp:7, - from /usr/include/boost/python/converter/arg_to_python.hpp:14, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object/class.hpp:9, - from /usr/include/boost/python/class.hpp:13, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/clash_ext.cpp:2: + from /usr/include/boost/python/converter/object_manager.hpp:8, + from /usr/include/boost/python/extract.hpp:10, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/indexing_ext.cpp:2: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -o lib/mmtbx_building_loop_closure_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_building_loop_closure_ext.so.0 mmtbx/building/loop_closure/ccd_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -liotbx_pdb -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, from /usr/include/boost/function/detail/prologue.hpp:12, from /usr/include/boost/function/function_template.hpp:13, @@ -16354,10 +16377,11 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/shared_types_ext.cpp:2: + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/asa_ext.cpp:2: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +g++ -o lib/mmtbx_building_loop_closure_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_building_loop_closure_ext.so.0 mmtbx/building/loop_closure/ccd_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -liotbx_pdb -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, from /usr/include/boost/function/detail/prologue.hpp:12, from /usr/include/boost/function/function_template.hpp:13, @@ -16365,18 +16389,30 @@ from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/converter/object_manager.hpp:8, - from /usr/include/boost/python/extract.hpp:10, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/indexing_ext.cpp:2: + from /usr/include/boost/python/converter/arg_to_python_base.hpp:7, + from /usr/include/boost/python/converter/arg_to_python.hpp:14, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/object/class.hpp:9, + from /usr/include/boost/python/class.hpp:13, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry/boost_python/shared_types_ext.cpp:2: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. Create symlinks for: 'lib/mmtbx_building_loop_closure_ext.so.0.0.1' 'lib/mmtbx_building_loop_closure_ext.so.0'->'lib/mmtbx_building_loop_closure_ext.so.0.0.1' 'lib/mmtbx_building_loop_closure_ext.so'->'lib/mmtbx_building_loop_closure_ext.so.0.0.1' g++ -o mmtbx/max_lik/max_lik_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/max_lik/max_lik_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_geometry_shared_types_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_shared_types_ext.so.0 mmtbx/geometry/boost_python/shared_types_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_geometry_primitive_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_primitive_ext.so.0 mmtbx/geometry/boost_python/primitive_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16385,12 +16421,12 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' - 'lib/mmtbx_geometry_shared_types_ext.so.0'->'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' - 'lib/mmtbx_geometry_shared_types_ext.so'->'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' +Create symlinks for: 'lib/mmtbx_geometry_primitive_ext.so.0.0.1' + 'lib/mmtbx_geometry_primitive_ext.so.0'->'lib/mmtbx_geometry_primitive_ext.so.0.0.1' + 'lib/mmtbx_geometry_primitive_ext.so'->'lib/mmtbx_geometry_primitive_ext.so.0.0.1' g++ -o mmtbx/max_lik/max_lik.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/max_lik/max_lik.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_geometry_primitive_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_primitive_ext.so.0 mmtbx/geometry/boost_python/primitive_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_geometry_shared_types_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_shared_types_ext.so.0 mmtbx/geometry/boost_python/shared_types_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16399,9 +16435,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_geometry_primitive_ext.so.0.0.1' - 'lib/mmtbx_geometry_primitive_ext.so.0'->'lib/mmtbx_geometry_primitive_ext.so.0.0.1' - 'lib/mmtbx_geometry_primitive_ext.so'->'lib/mmtbx_geometry_primitive_ext.so.0.0.1' +Create symlinks for: 'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' + 'lib/mmtbx_geometry_shared_types_ext.so.0'->'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' + 'lib/mmtbx_geometry_shared_types_ext.so'->'lib/mmtbx_geometry_shared_types_ext.so.0.0.1' g++ -o mmtbx/bulk_solvent/mosaic_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/bulk_solvent/mosaic_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_den_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_den_restraints_ext.so.0 mmtbx/den/boost_python/den_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm @@ -16419,6 +16455,7 @@ g++ -o mmtbx/ncs/cartesian_restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/ncs/cartesian_restraints_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_f_model_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_f_model_ext.so.0 mmtbx/f_model/f_model_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_geometry_sphere_surface_sampling_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_sphere_surface_sampling_ext.so.0 mmtbx/geometry/boost_python/sphere_surface_sampling_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16427,12 +16464,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_f_model_ext.so.0.0.1' - 'lib/mmtbx_f_model_ext.so.0'->'lib/mmtbx_f_model_ext.so.0.0.1' - 'lib/mmtbx_f_model_ext.so'->'lib/mmtbx_f_model_ext.so.0.0.1' -g++ -o mmtbx/ncs/tncs_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/ncs/tncs_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_geometry_sphere_surface_sampling_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_sphere_surface_sampling_ext.so.0 mmtbx/geometry/boost_python/sphere_surface_sampling_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16441,11 +16472,18 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/mmtbx_f_model_ext.so.0.0.1' + 'lib/mmtbx_f_model_ext.so.0'->'lib/mmtbx_f_model_ext.so.0.0.1' + 'lib/mmtbx_f_model_ext.so'->'lib/mmtbx_f_model_ext.so.0.0.1' Create symlinks for: 'lib/mmtbx_geometry_sphere_surface_sampling_ext.so.0.0.1' 'lib/mmtbx_geometry_sphere_surface_sampling_ext.so.0'->'lib/mmtbx_geometry_sphere_surface_sampling_ext.so.0.0.1' 'lib/mmtbx_geometry_sphere_surface_sampling_ext.so'->'lib/mmtbx_geometry_sphere_surface_sampling_ext.so.0.0.1' +g++ -o mmtbx/ncs/tncs_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/ncs/tncs_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o mmtbx/pair_interaction/interaction_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/pair_interaction/interaction_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o mmtbx/probe/boost_python/probe_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/probe/boost_python/probe_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_hydrogens_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_hydrogens_ext.so.0 mmtbx/hydrogens/hydrogens_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16458,8 +16496,6 @@ Create symlinks for: 'lib/mmtbx_hydrogens_ext.so.0.0.1' 'lib/mmtbx_hydrogens_ext.so.0'->'lib/mmtbx_hydrogens_ext.so.0.0.1' 'lib/mmtbx_hydrogens_ext.so'->'lib/mmtbx_hydrogens_ext.so.0.0.1' -g++ -o mmtbx/probe/boost_python/probe_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/probe/boost_python/probe_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o mmtbx/probe/Scoring.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/probe/Scoring.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_masks_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_masks_ext.so.0 mmtbx/masks/masks_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lmmtbx_masks -lcctbx_sgtbx_asu -lcctbx -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm @@ -16476,7 +16512,7 @@ 'lib/mmtbx_masks_ext.so'->'lib/mmtbx_masks_ext.so.0.0.1' g++ -o mmtbx/probe/DotSpheres.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/probe/DotSpheres.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_mosaic_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_mosaic_ext.so.0 mmtbx/bulk_solvent/mosaic_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_ncs_cartesian_restraints_ext.so.0 mmtbx/ncs/cartesian_restraints_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16485,12 +16521,12 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_mosaic_ext.so.0.0.1' - 'lib/mmtbx_mosaic_ext.so.0'->'lib/mmtbx_mosaic_ext.so.0.0.1' - 'lib/mmtbx_mosaic_ext.so'->'lib/mmtbx_mosaic_ext.so.0.0.1' +Create symlinks for: 'lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1' + 'lib/mmtbx_ncs_cartesian_restraints_ext.so.0'->'lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1' + 'lib/mmtbx_ncs_cartesian_restraints_ext.so'->'lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1' g++ -o mmtbx/probe/SpatialQuery.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/probe/SpatialQuery.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_ncs_cartesian_restraints_ext.so.0 mmtbx/ncs/cartesian_restraints_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_mosaic_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_mosaic_ext.so.0 mmtbx/bulk_solvent/mosaic_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16499,9 +16535,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1' - 'lib/mmtbx_ncs_cartesian_restraints_ext.so.0'->'lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1' - 'lib/mmtbx_ncs_cartesian_restraints_ext.so'->'lib/mmtbx_ncs_cartesian_restraints_ext.so.0.0.1' +Create symlinks for: 'lib/mmtbx_mosaic_ext.so.0.0.1' + 'lib/mmtbx_mosaic_ext.so.0'->'lib/mmtbx_mosaic_ext.so.0.0.1' + 'lib/mmtbx_mosaic_ext.so'->'lib/mmtbx_mosaic_ext.so.0.0.1' g++ -o mmtbx/geometry_restraints/boost_python/ramachandran_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry_restraints/boost_python/ramachandran_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_geometry_indexing_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_indexing_ext.so.0 mmtbx/geometry/boost_python/indexing_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm @@ -16515,12 +16551,11 @@ /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. g++ -o mmtbx/reduce/boost_python/reduce_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/reduce/boost_python/reduce_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/mmtbx_bulk_solvent_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_bulk_solvent_ext.so.0 mmtbx/bulk_solvent/bulk_solvent_ext.o mmtbx/bulk_solvent/bulk_solvent.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm Create symlinks for: 'lib/mmtbx_geometry_indexing_ext.so.0.0.1' 'lib/mmtbx_geometry_indexing_ext.so.0'->'lib/mmtbx_geometry_indexing_ext.so.0.0.1' 'lib/mmtbx_geometry_indexing_ext.so'->'lib/mmtbx_geometry_indexing_ext.so.0.0.1' g++ -o mmtbx/reduce/PositionReturn.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/reduce/PositionReturn.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_bulk_solvent_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_bulk_solvent_ext.so.0 mmtbx/bulk_solvent/bulk_solvent_ext.o mmtbx/bulk_solvent/bulk_solvent.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16529,10 +16564,8 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_max_lik_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_max_lik_ext.so.0 mmtbx/max_lik/max_lik_ext.o mmtbx/max_lik/max_lik.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/mmtbx_bulk_solvent_ext.so.0.0.1' - 'lib/mmtbx_bulk_solvent_ext.so.0'->'lib/mmtbx_bulk_solvent_ext.so.0.0.1' - 'lib/mmtbx_bulk_solvent_ext.so'->'lib/mmtbx_bulk_solvent_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16543,6 +16576,9 @@ /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. g++ -o mmtbx/reduce/InteractionGraph.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/reduce/InteractionGraph.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/mmtbx_bulk_solvent_ext.so.0.0.1' + 'lib/mmtbx_bulk_solvent_ext.so.0'->'lib/mmtbx_bulk_solvent_ext.so.0.0.1' + 'lib/mmtbx_bulk_solvent_ext.so'->'lib/mmtbx_bulk_solvent_ext.so.0.0.1' Create symlinks for: 'lib/mmtbx_max_lik_ext.so.0.0.1' 'lib/mmtbx_max_lik_ext.so.0'->'lib/mmtbx_max_lik_ext.so.0.0.1' 'lib/mmtbx_max_lik_ext.so'->'lib/mmtbx_max_lik_ext.so.0.0.1' @@ -16615,7 +16651,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -g++ -o lib/mmtbx_ncs_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_ncs_ext.so.0 mmtbx/ncs/tncs_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_geometry_clash_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_clash_ext.so.0 mmtbx/geometry/boost_python/clash_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16624,12 +16660,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_ncs_ext.so.0.0.1' - 'lib/mmtbx_ncs_ext.so.0'->'lib/mmtbx_ncs_ext.so.0.0.1' - 'lib/mmtbx_ncs_ext.so'->'lib/mmtbx_ncs_ext.so.0.0.1' -g++ -o mmtbx/rotamer/fit_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/rotamer/fit_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_geometry_clash_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_clash_ext.so.0 mmtbx/geometry/boost_python/clash_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_ncs_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_ncs_ext.so.0 mmtbx/ncs/tncs_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16641,8 +16672,14 @@ Create symlinks for: 'lib/mmtbx_geometry_clash_ext.so.0.0.1' 'lib/mmtbx_geometry_clash_ext.so.0'->'lib/mmtbx_geometry_clash_ext.so.0.0.1' 'lib/mmtbx_geometry_clash_ext.so'->'lib/mmtbx_geometry_clash_ext.so.0.0.1' +Create symlinks for: 'lib/mmtbx_ncs_ext.so.0.0.1' + 'lib/mmtbx_ncs_ext.so.0'->'lib/mmtbx_ncs_ext.so.0.0.1' + 'lib/mmtbx_ncs_ext.so'->'lib/mmtbx_ncs_ext.so.0.0.1' +g++ -o mmtbx/rotamer/fit_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/rotamer/fit_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o mmtbx/rsr/rsr_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/rsr/rsr_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +ar rc probe/lib/libprobelib.a mmtbx/probe/Scoring.o mmtbx/probe/DotSpheres.o mmtbx/probe/SpatialQuery.o In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/wyckoff.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/sym_equiv_sites.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/crystal/direct_space_asu.h:4, @@ -16654,11 +16691,9 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:100:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int i=0; i cctbx::geometry_restraints::shared_proxy_remove(const scitbx::af::const_ref&, const scitbx::af::const_ref&) [with ProxyType = mmtbx::geometry_restraints::reference_coordinate_proxy]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.cpp:80:41: required from here @@ -16667,7 +16702,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/geometry_restraints/proxy_select.h:187:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 187 | if (match_ctr != i_seqs.size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -/usr/lib/aarch64-linux-gnu/libboost_thread.soIn file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:6: +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/site_symmetry.h:6: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_3; std::size_t = long unsigned int]’ 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); @@ -16678,14 +16713,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ -: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h: In instantiation of ‘void cctbx::sgtbx::tensors::constraints::initialize(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:47:5: required from ‘cctbx::sgtbx::tensors::constraints::constraints(const scitbx::af::const_ref&, std::size_t, bool) [with FloatType = double; tensor_t = scitbx::matrix::tensors::tensor_rank_4; std::size_t = long unsigned int]’ 47 | initialize(symmetry_matrices, i_first_matrix_to_use, reciprocal_space); @@ -16696,11 +16723,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/sgtbx/tensors.h:185:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int j = 0; j < tensor_t::size(); j++) { | ~~^~~~~~~~~~~~~~~~~~ -Create symlinks for: 'lib/mmtbx_pair_interaction_ext.so.0.0.1' - 'lib/mmtbx_pair_interaction_ext.so.0'->'lib/mmtbx_pair_interaction_ext.so.0.0.1' - 'lib/mmtbx_pair_interaction_ext.so'->'lib/mmtbx_pair_interaction_ext.so.0.0.1' -g++ -o mmtbx/scaling/twinning_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/scaling/twinning_bpl.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_array.hpp:23, from /usr/include/boost/shared_array.hpp:17, @@ -16727,6 +16749,20 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +g++ -o lib/mmtbx_pair_interaction_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_pair_interaction_ext.so.0 mmtbx/pair_interaction/interaction_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/mmtbx_pair_interaction_ext.so.0.0.1' + 'lib/mmtbx_pair_interaction_ext.so.0'->'lib/mmtbx_pair_interaction_ext.so.0.0.1' + 'lib/mmtbx_pair_interaction_ext.so'->'lib/mmtbx_pair_interaction_ext.so.0.0.1' +g++ -o mmtbx/scaling/twinning_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/scaling/twinning_bpl.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o mmtbx/scaling/relative_scaling_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/scaling/relative_scaling_bpl.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o mmtbx/scaling/outlier_bpl.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/scaling/outlier_bpl.cpp @@ -16745,7 +16781,7 @@ 'lib/mmtbx_rsr_ext.so'->'lib/mmtbx_rsr_ext.so.0.0.1' g++ -o mmtbx/secondary_structure/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/ccp4 -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/secondary_structure/ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_geometry_asa_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_asa_ext.so.0 mmtbx/geometry/boost_python/asa_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_probe_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_probe_ext.so.0 mmtbx/probe/boost_python/probe_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Lprobe/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/probe/lib -lprobelib -liotbx_pdb -lcctbx -lscitbx_boost_python -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16754,6 +16790,12 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/mmtbx_probe_ext.so.0.0.1' + 'lib/mmtbx_probe_ext.so.0'->'lib/mmtbx_probe_ext.so.0.0.1' + 'lib/mmtbx_probe_ext.so'->'lib/mmtbx_probe_ext.so.0.0.1' +g++ -o mmtbx/tls/decompose_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/decompose_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/mmtbx_geometry_asa_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_geometry_asa_ext.so.0 mmtbx/geometry/boost_python/asa_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm g++ -o lib/mmtbx_reference_coordinate_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_reference_coordinate_ext.so.0 mmtbx/geometry_restraints/boost_python/reference_coordinate_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16763,13 +16805,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/mmtbx_probe_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_probe_ext.so.0 mmtbx/probe/boost_python/probe_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Lprobe/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/probe/lib -lprobelib -liotbx_pdb -lcctbx -lscitbx_boost_python -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -Create symlinks for: 'lib/mmtbx_geometry_asa_ext.so.0.0.1' - 'lib/mmtbx_geometry_asa_ext.so.0'->'lib/mmtbx_geometry_asa_ext.so.0.0.1' - 'lib/mmtbx_geometry_asa_ext.so'->'lib/mmtbx_geometry_asa_ext.so.0.0.1' -Create symlinks for: 'lib/mmtbx_reference_coordinate_ext.so.0.0.1' - 'lib/mmtbx_reference_coordinate_ext.so.0'->'lib/mmtbx_reference_coordinate_ext.so.0.0.1' - 'lib/mmtbx_reference_coordinate_ext.so'->'lib/mmtbx_reference_coordinate_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16778,16 +16813,15 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o mmtbx/tls/decompose_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/decompose_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/mmtbx_reference_coordinate_ext.so.0.0.1' + 'lib/mmtbx_reference_coordinate_ext.so.0'->'lib/mmtbx_reference_coordinate_ext.so.0.0.1' + 'lib/mmtbx_reference_coordinate_ext.so'->'lib/mmtbx_reference_coordinate_ext.so.0.0.1' g++ -o mmtbx/tls/tls_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/tls_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/mmtbx_probe_ext.so.0.0.1' - 'lib/mmtbx_probe_ext.so.0'->'lib/mmtbx_probe_ext.so.0.0.1' - 'lib/mmtbx_probe_ext.so'->'lib/mmtbx_probe_ext.so.0.0.1' -g++ -o mmtbx/tls/optimise_amplitudes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/optimise_amplitudes.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/mmtbx_rotamer_fit_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_rotamer_fit_ext.so.0 mmtbx/rotamer/fit_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/mmtbx_geometry_asa_ext.so.0.0.1' + 'lib/mmtbx_geometry_asa_ext.so.0'->'lib/mmtbx_geometry_asa_ext.so.0.0.1' + 'lib/mmtbx_geometry_asa_ext.so'->'lib/mmtbx_geometry_asa_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16796,14 +16830,14 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o mmtbx/tls/optimise_amplitudes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/optimise_amplitudes.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/mmtbx_rotamer_fit_ext.so.0.0.1' 'lib/mmtbx_rotamer_fit_ext.so.0'->'lib/mmtbx_rotamer_fit_ext.so.0.0.1' 'lib/mmtbx_rotamer_fit_ext.so'->'lib/mmtbx_rotamer_fit_ext.so.0.0.1' g++ -o mmtbx/tls/optimise_amplitudes_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/optimise_amplitudes_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o mmtbx/tls/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/utils.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_secondary_structure_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_secondary_structure_ext.so.0 mmtbx/secondary_structure/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_ramachandran_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_ramachandran_restraints_ext.so.0 mmtbx/geometry_restraints/boost_python/ramachandran_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16812,12 +16846,13 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_secondary_structure_ext.so.0.0.1' - 'lib/mmtbx_secondary_structure_ext.so.0'->'lib/mmtbx_secondary_structure_ext.so.0.0.1' - 'lib/mmtbx_secondary_structure_ext.so'->'lib/mmtbx_secondary_structure_ext.so.0.0.1' -g++ -o mmtbx/tls/utils_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/utils_ext.cpp +g++ -o mmtbx/tls/utils.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/utils.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_ramachandran_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_ramachandran_restraints_ext.so.0 mmtbx/geometry_restraints/boost_python/ramachandran_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_secondary_structure_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_secondary_structure_ext.so.0 mmtbx/secondary_structure/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -liotbx_pdb -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/mmtbx_ramachandran_restraints_ext.so.0.0.1' + 'lib/mmtbx_ramachandran_restraints_ext.so.0'->'lib/mmtbx_ramachandran_restraints_ext.so.0.0.1' + 'lib/mmtbx_ramachandran_restraints_ext.so'->'lib/mmtbx_ramachandran_restraints_ext.so.0.0.1' +g++ -o mmtbx/tls/utils_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/tls/utils_ext.cpp /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16826,9 +16861,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_ramachandran_restraints_ext.so.0.0.1' - 'lib/mmtbx_ramachandran_restraints_ext.so.0'->'lib/mmtbx_ramachandran_restraints_ext.so.0.0.1' - 'lib/mmtbx_ramachandran_restraints_ext.so'->'lib/mmtbx_ramachandran_restraints_ext.so.0.0.1' +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/mmtbx_secondary_structure_ext.so.0.0.1' + 'lib/mmtbx_secondary_structure_ext.so.0'->'lib/mmtbx_secondary_structure_ext.so.0.0.1' + 'lib/mmtbx_secondary_structure_ext.so'->'lib/mmtbx_secondary_structure_ext.so.0.0.1' g++ -o mmtbx/utils/utils_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/utils/utils_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ ar rc reduce/lib/libreduce2lib.a mmtbx/reduce/PositionReturn.o mmtbx/reduce/InteractionGraph.o mmtbx/reduce/Optimizers.o @@ -16864,12 +16900,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o lib/omptbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=omptbx_ext.so.0 omptbx/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lomptbx -lboost_thread -lboost_system -lboost_python313 -lm Create symlinks for: 'lib/mmtbx_tls_optimise_amplitudes_ext.so.0.0.1' 'lib/mmtbx_tls_optimise_amplitudes_ext.so.0'->'lib/mmtbx_tls_optimise_amplitudes_ext.so.0.0.1' 'lib/mmtbx_tls_optimise_amplitudes_ext.so'->'lib/mmtbx_tls_optimise_amplitudes_ext.so.0.0.1' -g++ -o rstbx/bpcx/detector_model/detector_model_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/bpcx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/src -Irstbx/bpcx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/detector_model/detector_model_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/omptbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=omptbx_ext.so.0 omptbx/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lomptbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -16881,8 +16915,10 @@ Create symlinks for: 'lib/omptbx_ext.so.0.0.1' 'lib/omptbx_ext.so.0'->'lib/omptbx_ext.so.0.0.1' 'lib/omptbx_ext.so'->'lib/omptbx_ext.so.0.0.1' +g++ -o rstbx/bpcx/detector_model/detector_model_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/bpcx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/src -Irstbx/bpcx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/detector_model/detector_model_ext.cpp g++ -o rstbx/bpcx/detector_model/sensor.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/bpcx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/src -Irstbx/bpcx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/bpcx/detector_model/sensor.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -17035,9 +17071,6 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_scaling_ext.so.0.0.1' - 'lib/mmtbx_scaling_ext.so.0'->'lib/mmtbx_scaling_ext.so.0.0.1' - 'lib/mmtbx_scaling_ext.so'->'lib/mmtbx_scaling_ext.so.0.0.1' In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -17070,8 +17103,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o rstbx/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -17150,6 +17181,11 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Create symlinks for: 'lib/mmtbx_scaling_ext.so.0.0.1' + 'lib/mmtbx_scaling_ext.so.0'->'lib/mmtbx_scaling_ext.so.0.0.1' + 'lib/mmtbx_scaling_ext.so'->'lib/mmtbx_scaling_ext.so.0.0.1' +g++ -o rstbx/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/src -Irstbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/diffraction/fastbragg/fastbragg.h: In member function ‘scitbx::af::versa > rstbx::diffraction::fastbragg::detector::intdata()’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/diffraction/fastbragg/fastbragg.h:89:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::versa_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for (int count = 0; count < raw.size(); ++count){ @@ -17176,7 +17212,7 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~ g++ -o rstbx/indexing_api/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/indexing_api/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/indexing_api/src -Irstbx/indexing_api/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/indexing_api/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/indexing_api/ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_validation_ramachandran_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_validation_ramachandran_ext.so.0 mmtbx/validation/ramachandran/rama_eval_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_utils_ext.so.0 mmtbx/utils/utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17185,14 +17221,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_validation_ramachandran_ext.so.0.0.1' - 'lib/mmtbx_validation_ramachandran_ext.so.0'->'lib/mmtbx_validation_ramachandran_ext.so.0.0.1' - 'lib/mmtbx_validation_ramachandran_ext.so'->'lib/mmtbx_validation_ramachandran_ext.so.0.0.1' -g++ -o rstbx/apps/integration_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/apps/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/apps/src -Irstbx/apps/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/apps/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/apps/integration_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o rstbx/simage/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/simage/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/src -Irstbx/simage/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_utils_ext.so.0 mmtbx/utils/utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_validation_ramachandran_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_validation_ramachandran_ext.so.0 mmtbx/validation/ramachandran/rama_eval_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +Create symlinks for: 'lib/mmtbx_utils_ext.so.0.0.1' + 'lib/mmtbx_utils_ext.so.0'->'lib/mmtbx_utils_ext.so.0.0.1' + 'lib/mmtbx_utils_ext.so'->'lib/mmtbx_utils_ext.so.0.0.1' /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17201,9 +17233,15 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_utils_ext.so.0.0.1' - 'lib/mmtbx_utils_ext.so.0'->'lib/mmtbx_utils_ext.so.0.0.1' - 'lib/mmtbx_utils_ext.so'->'lib/mmtbx_utils_ext.so.0.0.1' +Create symlinks for: 'lib/mmtbx_validation_ramachandran_ext.so.0.0.1' + 'lib/mmtbx_validation_ramachandran_ext.so.0'->'lib/mmtbx_validation_ramachandran_ext.so.0.0.1' + 'lib/mmtbx_validation_ramachandran_ext.so'->'lib/mmtbx_validation_ramachandran_ext.so.0.0.1' +g++ -o rstbx/apps/integration_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/apps/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/apps/src -Irstbx/apps/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/apps/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/apps/integration_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o rstbx/simage/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/simage/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/src -Irstbx/simage/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o rstbx/simulation/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/simulation/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/src -Irstbx/simulation/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/diffraction/fastbragg/fastbragg_ext.cpp:10: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/diffraction/fastbragg/fastbragg.h: In member function ‘scitbx::af::versa > rstbx::diffraction::fastbragg::detector::intdata()’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/diffraction/fastbragg/fastbragg.h:89:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::versa_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] @@ -17295,9 +17333,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/diffraction/fastbragg/fastbragg.h:456:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 456 | for(int i_lambda=0; i_lambda < lambdas.size(); ++i_lambda){ | ~~~~~~~~~^~~~~~~~~~~~~~~~ -g++ -o rstbx/simulation/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/annlib_adaptbx/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/src -Irstbx/simulation/src -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/src -Irstbx/simulation/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/rstbx_bpcx_detector_model_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_bpcx_detector_model_ext.so.0 rstbx/bpcx/detector_model/detector_model_ext.o rstbx/bpcx/detector_model/sensor.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); @@ -17319,6 +17354,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ +g++ -o lib/rstbx_bpcx_detector_model_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_bpcx_detector_model_ext.so.0 rstbx/bpcx/detector_model/detector_model_ext.o rstbx/bpcx/detector_model/sensor.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17458,22 +17494,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/indexing_api/ext.cpp:135:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 135 | for (int i = 0; i < gradients.size(); ++i){ | ~~^~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/ext.cpp:2: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/image_simple.hpp: In member function ‘rstbx::simage::image_simple& rstbx::simage::image_simple::compute(const cctbx::uctbx::unit_cell&, const scitbx::af::const_ref >&, const scitbx::af::const_ref&, const scitbx::mat3&, double, double, int, double, scitbx::vec2, scitbx::vec2, unsigned int, double)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/image_simple.hpp:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 144 | for(int i=0;i<=point_spread;i++) { - | ~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/image_simple.hpp:148:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 148 | for(int j=0;j<=point_spread;j++) { - | ~^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/image_simple.hpp:10: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/ext.cpp: In function ‘std::string rstbx::simage::ext::combine_rgb_images(const boost::python::list&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/ext.cpp:58:42: warning: comparison of integer expressions of different signedness: ‘boost::python::ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 58 | TBXX_ASSERT(bp::len(rgb_images[j]) == img_size); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/tbxx/error_utils.hpp:59:9: note: in definition of macro ‘TBXX_ASSERT’ - 59 | if (!(condition)) { \ - | ^~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/libdistl.h:81, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/spotfinder/core_toolbox/distl.h:14, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/apps/stills/simple_integration.h:9, @@ -17526,11 +17546,27 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/apps/stills/simple_integration.h:638:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 638 | for (int k=0; k >&, const scitbx::af::const_ref&, const scitbx::mat3&, double, double, int, double, scitbx::vec2, scitbx::vec2, unsigned int, double)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/image_simple.hpp:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 144 | for(int i=0;i<=point_spread;i++) { + | ~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/image_simple.hpp:148:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 148 | for(int j=0;j<=point_spread;j++) { + | ~^~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/ext.cpp:11: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/sim_xfel1.h: In member function ‘scitbx::af::shared rstbx::xfel1::select_proximal_indices(const int&, const double&, const double&, const cctbx::crystal_orientation&, const double&, const double&, const double&, const double&)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/sim_xfel1.h:113:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::shared_plain >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 113 | for (int x = 0; x < indices_all.size(); ++x){ | ~~^~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/image_simple.hpp:10: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/ext.cpp: In function ‘std::string rstbx::simage::ext::combine_rgb_images(const boost::python::list&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simage/ext.cpp:58:42: warning: comparison of integer expressions of different signedness: ‘boost::python::ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 58 | TBXX_ASSERT(bp::len(rgb_images[j]) == img_size); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/tbxx/error_utils.hpp:59:9: note: in definition of macro ‘TBXX_ASSERT’ + 59 | if (!(condition)) { \ + | ^~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/sim_xfel1.h: In member function ‘scitbx::af::versa > rstbx::xfel1::raw_diffraction(scitbx::af::shared, scitbx::af::versa >, const size_t&, const double&, const double&, const double&)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/rstbx/simulation/sim_xfel1.h:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 178 | for (int mcount=0; mcount::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 231 | for (int imos = 0; imos < mosaic_perturbations.size(); ++imos){ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/rstbx_bandpass_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_bandpass_ext.so.0 rstbx/bandpass/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lann-cctbx -lann_adaptor -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/mmtbx_tls_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_tls_ext.so.0 mmtbx/tls/tls_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, @@ -17558,24 +17592,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:175:26: note: ‘’ declared here 175 | resize(new_size, ElementType()); | ^~~~~~~~~~~~~ -/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h: In member function ‘void scitbx::af::shared_plain::resize(const size_type&) [with ElementType = cctbx::crystal_orientation]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:175:15: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 175 | resize(new_size, ElementType()); @@ -17586,17 +17602,23 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:175:26: note: ‘’ declared here 175 | resize(new_size, ElementType()); | ^~~~~~~~~~~~~ +g++ -o lib/rstbx_bandpass_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_bandpass_ext.so.0 rstbx/bandpass/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lann-cctbx -lann_adaptor -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. Create symlinks for: 'lib/rstbx_bandpass_ext.so.0.0.1' 'lib/rstbx_bandpass_ext.so.0'->'lib/rstbx_bandpass_ext.so.0.0.1' 'lib/rstbx_bandpass_ext.so'->'lib/rstbx_bandpass_ext.so.0.0.1' g++ -o scitbx/array_family/boost_python/flex_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/mmtbx_tls_ext.so.0.0.1' - 'lib/mmtbx_tls_ext.so.0'->'lib/mmtbx_tls_ext.so.0.0.1' - 'lib/mmtbx_tls_ext.so'->'lib/mmtbx_tls_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_grid.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_grid.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/mmtbx_reduce_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_reduce_ext.so.0 mmtbx/reduce/boost_python/reduce_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Lreduce/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/reduce/lib -Lprobe/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/probe/lib -lreduce2lib -lprobelib -liotbx_pdb -lcctbx -lscitbx_boost_python -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/mmtbx_tls_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_tls_ext.so.0 mmtbx/tls/tls_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17605,11 +17627,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/mmtbx_reduce_ext.so.0.0.1' - 'lib/mmtbx_reduce_ext.so.0'->'lib/mmtbx_reduce_ext.so.0.0.1' - 'lib/mmtbx_reduce_ext.so'->'lib/mmtbx_reduce_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_bool.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_bool.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/mmtbx_reduce_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_reduce_ext.so.0 mmtbx/reduce/boost_python/reduce_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Lreduce/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/reduce/lib -Lprobe/lib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/probe/lib -lreduce2lib -lprobelib -liotbx_pdb -lcctbx -lscitbx_boost_python -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm g++ -o lib/rstbx_symmetry_constraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_symmetry_constraints_ext.so.0 rstbx/symmetry/constraints/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17620,14 +17638,14 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/mmtbx_tls_ext.so.0.0.1' + 'lib/mmtbx_tls_ext.so.0'->'lib/mmtbx_tls_ext.so.0.0.1' + 'lib/mmtbx_tls_ext.so'->'lib/mmtbx_tls_ext.so.0.0.1' +g++ -o scitbx/array_family/boost_python/flex_grid.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_grid.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/rstbx_symmetry_constraints_ext.so.0.0.1' 'lib/rstbx_symmetry_constraints_ext.so.0'->'lib/rstbx_symmetry_constraints_ext.so.0.0.1' 'lib/rstbx_symmetry_constraints_ext.so'->'lib/rstbx_symmetry_constraints_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_size_t.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/rstbx_simage_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_simage_ext.so.0 rstbx/simage/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/rstbx_indexing_api_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_indexing_api_ext.so.0 rstbx/indexing_api/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17636,6 +17654,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o scitbx/array_family/boost_python/flex_bool.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_bool.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/rstbx_simage_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_simage_ext.so.0 rstbx/simage/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17648,12 +17669,12 @@ Create symlinks for: 'lib/rstbx_simage_ext.so.0.0.1' 'lib/rstbx_simage_ext.so.0'->'lib/rstbx_simage_ext.so.0.0.1' 'lib/rstbx_simage_ext.so'->'lib/rstbx_simage_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_int.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp +g++ -o scitbx/array_family/boost_python/flex_size_t.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/rstbx_indexing_api_ext.so.0.0.1' - 'lib/rstbx_indexing_api_ext.so.0'->'lib/rstbx_indexing_api_ext.so.0.0.1' - 'lib/rstbx_indexing_api_ext.so'->'lib/rstbx_indexing_api_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_float.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_float.cpp +Create symlinks for: 'lib/mmtbx_reduce_ext.so.0.0.1' + 'lib/mmtbx_reduce_ext.so.0'->'lib/mmtbx_reduce_ext.so.0.0.1' + 'lib/mmtbx_reduce_ext.so'->'lib/mmtbx_reduce_ext.so.0.0.1' +g++ -o scitbx/array_family/boost_python/flex_int.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/rstbx_simulation_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_simulation_ext.so.0 rstbx/simulation/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17668,9 +17689,24 @@ Create symlinks for: 'lib/rstbx_simulation_ext.so.0.0.1' 'lib/rstbx_simulation_ext.so.0'->'lib/rstbx_simulation_ext.so.0.0.1' 'lib/rstbx_simulation_ext.so'->'lib/rstbx_simulation_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp +g++ -o scitbx/array_family/boost_python/flex_float.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_float.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/rstbx_indexing_api_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_indexing_api_ext.so.0 rstbx/indexing_api/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/rstbx_indexing_api_ext.so.0.0.1' + 'lib/rstbx_indexing_api_ext.so.0'->'lib/rstbx_indexing_api_ext.so.0.0.1' + 'lib/rstbx_indexing_api_ext.so'->'lib/rstbx_indexing_api_ext.so.0.0.1' g++ -o lib/rstbx_diffraction_fastbragg_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_diffraction_fastbragg_ext.so.0 rstbx/diffraction/fastbragg/fastbragg_ext.o rstbx/diffraction/fastbragg/fastbragg.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o scitbx/array_family/boost_python/flex_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -17680,6 +17716,11 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/rstbx_diffraction_fastbragg_ext.so.0.0.1' + 'lib/rstbx_diffraction_fastbragg_ext.so.0'->'lib/rstbx_diffraction_fastbragg_ext.so.0.0.1' + 'lib/rstbx_diffraction_fastbragg_ext.so'->'lib/rstbx_diffraction_fastbragg_ext.so.0.0.1' +g++ -o scitbx/array_family/boost_python/flex_double_matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_ext.cpp: In member function ‘const char* scitbx::af::boost_python::cost_of_m_handle_in_af_shared::operator()(unsigned int, unsigned int)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_ext.cpp:367:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 367 | for(int n=0; n < n_repeats; ++n) { @@ -17690,9 +17731,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_ext.cpp:383:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 383 | for(int n=0; n < n_repeats; ++n) { | ~~^~~~~~~~~~~ -Create symlinks for: 'lib/rstbx_diffraction_fastbragg_ext.so.0.0.1' - 'lib/rstbx_diffraction_fastbragg_ext.so.0'->'lib/rstbx_diffraction_fastbragg_ext.so.0.0.1' - 'lib/rstbx_diffraction_fastbragg_ext.so'->'lib/rstbx_diffraction_fastbragg_ext.so.0.0.1' In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, @@ -17713,8 +17751,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/selections.h:156:7: note: in expansion of macro ‘SCITBX_ASSERT’ 156 | SCITBX_ASSERT(iselection[i] < selectee_size); | ^~~~~~~~~~~~~ -g++ -o scitbx/array_family/boost_python/flex_double_matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_ptr.hpp:25, from /usr/include/boost/shared_ptr.hpp:17, @@ -19285,6 +19321,22 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +g++ -o lib/rstbx_integration_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_integration_ext.so.0 rstbx/apps/integration_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lann-cctbx -lann_adaptor -lspotfinder -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/rstbx_integration_ext.so.0.0.1' + 'lib/rstbx_integration_ext.so.0'->'lib/rstbx_integration_ext.so.0.0.1' + 'lib/rstbx_integration_ext.so'->'lib/rstbx_integration_ext.so.0.0.1' +g++ -o scitbx/array_family/boost_python/flex_complex_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, @@ -19349,6 +19401,21 @@ /usr/include/c++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:1: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ^~~~~~~~~~~~~ In file included from /usr/include/c++/15/cassert:46, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -19607,7 +19674,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); | ^~~~~~~~~~~~~ -g++ -o lib/rstbx_integration_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_integration_ext.so.0 rstbx/apps/integration_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lann-cctbx -lann_adaptor -lspotfinder -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = bool]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = bool]’ 119 | detail::copy_to_slice_detail(self, slices, other); @@ -19682,16 +19748,24 @@ | ~~~~~~~~~~^~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; -/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h: In instantiation of ‘scitbx::af::shared scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here + 311 | def( \ + | ~~~^~~ + 312 | #pyname"_from_byte_str", \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 313 | shared_from_byte_str, \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 314 | (arg("byte_str"))); \ + | ~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); + | ^~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::first_index_a_s(const f_t&, e_t) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = long unsigned int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:963:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 963 | def("first_index", first_index_a_s); @@ -19738,11 +19812,42 @@ /usr/include/c++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -Create symlinks for: 'lib/rstbx_integration_ext.so.0.0.1' - 'lib/rstbx_integration_ext.so.0'->'lib/rstbx_integration_ext.so.0.0.1' - 'lib/rstbx_integration_ext.so'->'lib/rstbx_integration_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_complex_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h: In instantiation of ‘scitbx::af::shared scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = long int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here + 311 | def( \ + | ~~~^~~ + 312 | #pyname"_from_byte_str", \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 313 | shared_from_byte_str, \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 314 | (arg("byte_str"))); \ + | ~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); + | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h: In instantiation of ‘scitbx::af::shared scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = signed char]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here + 311 | def( \ + | ~~~^~~ + 312 | #pyname"_from_byte_str", \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 313 | shared_from_byte_str, \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 314 | (arg("byte_str"))); \ + | ~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); + | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, @@ -19758,88 +19863,76 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:1: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h: In instantiation of ‘scitbx::af::shared scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = short int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here + 311 | def( \ + | ~~~^~~ + 312 | #pyname"_from_byte_str", \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 313 | shared_from_byte_str, \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 314 | (arg("byte_str"))); \ + | ~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/15/cassert:46, - from /usr/include/boost/move/detail/type_traits.hpp:33, - from /usr/include/boost/move/traits.hpp:31, - from /usr/include/boost/move/utility.hpp:30, - from /usr/include/boost/optional/optional.hpp:59, - from /usr/include/boost/optional.hpp:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref_reductions.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 769 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 770 | shared_plain, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 771 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 772 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); + | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::first_index_a_s(const f_t&, e_t) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:963:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 963 | def("first_index", first_index_a_s); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here - 105 | flex_wrapper::integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 773 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 774 | shared, - | ~~~~~~~~~~~~~~~~~~~~ - 775 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 776 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1048:21: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::signed_integer(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1048 | return integer(python_name, flex_root_scope); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here + 242 | flex_wrapper::signed_integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_function.h:1441, + from /usr/include/c++/15/functional:51, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:15, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/to_python_value.hpp:14, + from /usr/include/boost/python/default_call_policies.hpp:10, + from /usr/include/boost/python/make_function.hpp:10, + from /usr/include/boost/python/def.hpp:11, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: +/usr/include/c++/15/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::last_index_a_s(const f_t&, e_t) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:964:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 964 | def("last_index", last_index_a_s); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here - 105 | flex_wrapper::integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1048:21: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::signed_integer(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1048 | return integer(python_name, flex_root_scope); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here + 242 | flex_wrapper::signed_integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::first_index_a_s(const f_t&, e_t) [with ElementType = float; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = float]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:963:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = float; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 963 | def("first_index", first_index_a_s); @@ -19886,67 +19979,195 @@ /usr/include/c++/15/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 769 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 770 | shared_plain, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 771 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 772 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1031 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here - 105 | flex_wrapper::integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 773 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 774 | shared, - | ~~~~~~~~~~~~~~~~~~~~ - 775 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 776 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1031 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here - 105 | flex_wrapper::integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:4: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h: In instantiation of ‘FloatType scitbx::matrix::norm_1(const scitbx::af::const_ref >&) [with FloatType = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:119:74: required from here + 119 | double (*matrix_norm_1)(const_ref const &) = matrix::norm_1; + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h:16:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 16 | for (int i=0; i >&) [with FloatType = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:177:11: required from here + 145 | class_f_t + | ~~~~~~~~~ + 146 | .def("is_square_matrix", is_square_matrix) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 147 | .def("matrix_diagonal", + | ~~~~~~~~~~~~~~~~~~~~~~~ + 148 | (shared(*)( + | ~~~~~~~~~~~~~~~~~~~ + 149 | const_ref > const&)) matrix_diagonal) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 150 | .def("matrix_upper_bidiagonal", matrix_upper_bidiagonal) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 151 | .def("matrix_lower_bidiagonal", matrix_lower_bidiagonal) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 152 | .def("matrix_diagonal_set_in_place", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 153 | (void(*)( + | ~~~~~~~~~ + 154 | ref > const&, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 155 | double const&)) matrix_diagonal_set_in_place, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 156 | arg("value")) + | ~~~~~~~~~~~~~ + 157 | .def("matrix_diagonal_set_in_place", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 158 | (void(*)( + | ~~~~~~~~~ + 159 | ref > const&, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 160 | const_ref const&)) matrix_diagonal_set_in_place, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 161 | arg("diagonal")) + | ~~~~~~~~~~~~~~~~ + 162 | .def("matrix_diagonal_add_in_place", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 163 | (void(*)( + | ~~~~~~~~~ + 164 | ref > const&, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 165 | double const&)) matrix_diagonal_add_in_place, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 166 | arg("value")) + | ~~~~~~~~~~~~~ + 167 | .def("matrix_diagonal_sum", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 168 | (double(*)( + | ~~~~~~~~~~~ + 169 | const_ref > const&)) matrix_diagonal_sum) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 170 | .def("matrix_trace", + | ~~~~~~~~~~~~~~~~~~~~ + 171 | (double(*)( + | ~~~~~~~~~~~ + 172 | const_ref > const&)) matrix_diagonal_sum) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 173 | .def("matrix_diagonal_product", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 174 | (double(*)( + | ~~~~~~~~~~~ + 175 | const_ref > const&)) matrix_diagonal_product) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 176 | .def("matrix_norm_1", matrix_norm_1) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 177 | .def("matrix_norm_inf", matrix::norm_inf) + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h:32:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 32 | for (int i=0; i >&) [with FloatType = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:178:11: required from here + 145 | class_f_t + | ~~~~~~~~~ + 146 | .def("is_square_matrix", is_square_matrix) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 147 | .def("matrix_diagonal", + | ~~~~~~~~~~~~~~~~~~~~~~~ + 148 | (shared(*)( + | ~~~~~~~~~~~~~~~~~~~ + 149 | const_ref > const&)) matrix_diagonal) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 150 | .def("matrix_upper_bidiagonal", matrix_upper_bidiagonal) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 151 | .def("matrix_lower_bidiagonal", matrix_lower_bidiagonal) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 152 | .def("matrix_diagonal_set_in_place", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 153 | (void(*)( + | ~~~~~~~~~ + 154 | ref > const&, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 155 | double const&)) matrix_diagonal_set_in_place, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 156 | arg("value")) + | ~~~~~~~~~~~~~ + 157 | .def("matrix_diagonal_set_in_place", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 158 | (void(*)( + | ~~~~~~~~~ + 159 | ref > const&, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 160 | const_ref const&)) matrix_diagonal_set_in_place, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 161 | arg("diagonal")) + | ~~~~~~~~~~~~~~~~ + 162 | .def("matrix_diagonal_add_in_place", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 163 | (void(*)( + | ~~~~~~~~~ + 164 | ref > const&, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 165 | double const&)) matrix_diagonal_add_in_place, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 166 | arg("value")) + | ~~~~~~~~~~~~~ + 167 | .def("matrix_diagonal_sum", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 168 | (double(*)( + | ~~~~~~~~~~~ + 169 | const_ref > const&)) matrix_diagonal_sum) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 170 | .def("matrix_trace", + | ~~~~~~~~~~~~~~~~~~~~ + 171 | (double(*)( + | ~~~~~~~~~~~ + 172 | const_ref > const&)) matrix_diagonal_sum) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 173 | .def("matrix_diagonal_product", + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 174 | (double(*)( + | ~~~~~~~~~~~ + 175 | const_ref > const&)) matrix_diagonal_product) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 176 | .def("matrix_norm_1", matrix_norm_1) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 177 | .def("matrix_norm_inf", matrix::norm_inf) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 178 | .def("matrix_norm_frobenius", matrix::norm_frobenius) + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h:46:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 46 | for (int k=0; k < a_ij.size(); ++k) norm_accu(a_ij[k]); + | ~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:1: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/15/cassert:46, + from /usr/include/boost/move/detail/type_traits.hpp:33, + from /usr/include/boost/move/traits.hpp:31, + from /usr/include/boost/move/utility.hpp:30, + from /usr/include/boost/optional/optional.hpp:59, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 769 | scitbx::boost_python::container_conversions::from_python_sequence< | ^~~~~~~~~~~~~~~~~~~~~ 770 | shared_plain, @@ -19955,26 +20176,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 | ::variable_capacity_policy>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 773 | scitbx::boost_python::container_conversions::from_python_sequence< | ^~~~~~~~~~~~~~~~~~~~~ 774 | shared, @@ -19983,16 +20204,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 776 | ::variable_capacity_policy>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] @@ -20065,11 +20286,11 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 769 | scitbx::boost_python::container_conversions::from_python_sequence< | ^~~~~~~~~~~~~~~~~~~~~ 770 | shared_plain, @@ -20078,44 +20299,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 772 | ::variable_capacity_policy>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h: In instantiation of ‘scitbx::af::shared scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here - 311 | def( \ - | ~~~^~~ - 312 | #pyname"_from_byte_str", \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 313 | shared_from_byte_str, \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 314 | (arg("byte_str"))); \ - | ~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); - | ^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 773 | scitbx::boost_python::container_conversions::from_python_sequence< | ^~~~~~~~~~~~~~~~~~~~~ 774 | shared, @@ -20124,39 +20327,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 776 | ::variable_capacity_policy>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h: In instantiation of ‘scitbx::af::shared scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = long int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:320:3: required from here - 311 | def( \ - | ~~~^~~ - 312 | #pyname"_from_byte_str", \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 313 | shared_from_byte_str, \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 314 | (arg("byte_str"))); \ - | ~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); - | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = float]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = float; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -20231,24 +20416,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for (int i=0;i scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = signed char]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:321:3: required from here - 311 | def( \ - | ~~~^~~ - 312 | #pyname"_from_byte_str", \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 313 | shared_from_byte_str, \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 314 | (arg("byte_str"))); \ - | ~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); - | ^~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = float]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = float; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); @@ -20330,194 +20497,62 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | for (int i=0;i scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = short int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:322:3: required from here - 311 | def( \ - | ~~~^~~ - 312 | #pyname"_from_byte_str", \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 313 | shared_from_byte_str, \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 314 | (arg("byte_str"))); \ - | ~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); - | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:1: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 202 | return copy_slice(self, slices_simple); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 782 | result - | ~~~~~~ - 783 | .def(init const&, optional >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 784 | .def(init >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 785 | .def(init const&>()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 786 | .def("element_size", element_size) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 787 | .staticmethod("element_size") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 788 | .def("accessor", accessor) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 789 | .def("nd", nd) - | ~~~~~~~~~~~~~~ - 790 | .def("is_0_based", is_0_based) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 791 | .def("origin", origin) - | ~~~~~~~~~~~~~~~~~~~~~~ - 792 | .def("all", all) - | ~~~~~~~~~~~~~~~~ - 793 | .def("last", last_0) - | ~~~~~~~~~~~~~~~~~~~~ - 794 | .def("last", last_1) - | ~~~~~~~~~~~~~~~~~~~~ - 795 | .def("is_padded", is_padded) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 796 | .def("focus", focus_0) - | ~~~~~~~~~~~~~~~~~~~~~~ - 797 | .def("focus", focus_1) - | ~~~~~~~~~~~~~~~~~~~~~~ - 798 | .def("focus_size_1d", focus_size_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 799 | .def("is_trivial_1d", is_trivial_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | .def("shift_origin", shift_origin) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | .def("id", id) - | ~~~~~~~~~~~~~~ - 802 | .def("size", size) - | ~~~~~~~~~~~~~~~~~~ - 803 | .def("__len__", size) - | ~~~~~~~~~~~~~~~~~~~~~ - 804 | .def("__sizeof__", memory_footprint) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 805 | .def("capacity", capacity) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 769 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 770 | shared_plain, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 771 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 772 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ - 269 | copy_to_slice(self, slices_simple, other.const_ref()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 289 | setitem_nd_slice(a, slices, b); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 782 | result - | ~~~~~~ - 783 | .def(init const&, optional >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 784 | .def(init >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 785 | .def(init const&>()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 786 | .def("element_size", element_size) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 787 | .staticmethod("element_size") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 788 | .def("accessor", accessor) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 789 | .def("nd", nd) - | ~~~~~~~~~~~~~~ - 790 | .def("is_0_based", is_0_based) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 791 | .def("origin", origin) - | ~~~~~~~~~~~~~~~~~~~~~~ - 792 | .def("all", all) - | ~~~~~~~~~~~~~~~~ - 793 | .def("last", last_0) - | ~~~~~~~~~~~~~~~~~~~~ - 794 | .def("last", last_1) - | ~~~~~~~~~~~~~~~~~~~~ - 795 | .def("is_padded", is_padded) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 796 | .def("focus", focus_0) - | ~~~~~~~~~~~~~~~~~~~~~~ - 797 | .def("focus", focus_1) - | ~~~~~~~~~~~~~~~~~~~~~~ - 798 | .def("focus_size_1d", focus_size_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 799 | .def("is_trivial_1d", is_trivial_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | .def("shift_origin", shift_origin) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | .def("id", id) - | ~~~~~~~~~~~~~~ - 802 | .def("size", size) - | ~~~~~~~~~~~~~~~~~~ - 803 | .def("__len__", size) - | ~~~~~~~~~~~~~~~~~~~~~ - 804 | .def("__sizeof__", memory_footprint) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 805 | .def("capacity", capacity) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 807 | .def("__getitem__", getitem_1d_slice) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 773 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 774 | shared, + | ~~~~~~~~~~~~~~~~~~~~ + 775 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 776 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = float]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = float]’ 119 | detail::copy_to_slice_detail(self, slices, other); @@ -20601,383 +20636,32 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned char]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 202 | return copy_slice(self, slices_simple); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 782 | result - | ~~~~~~ - 783 | .def(init const&, optional >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 784 | .def(init >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 785 | .def(init const&>()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 786 | .def("element_size", element_size) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 787 | .staticmethod("element_size") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 788 | .def("accessor", accessor) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 789 | .def("nd", nd) - | ~~~~~~~~~~~~~~ - 790 | .def("is_0_based", is_0_based) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 791 | .def("origin", origin) - | ~~~~~~~~~~~~~~~~~~~~~~ - 792 | .def("all", all) - | ~~~~~~~~~~~~~~~~ - 793 | .def("last", last_0) - | ~~~~~~~~~~~~~~~~~~~~ - 794 | .def("last", last_1) - | ~~~~~~~~~~~~~~~~~~~~ - 795 | .def("is_padded", is_padded) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 796 | .def("focus", focus_0) - | ~~~~~~~~~~~~~~~~~~~~~~ - 797 | .def("focus", focus_1) - | ~~~~~~~~~~~~~~~~~~~~~~ - 798 | .def("focus_size_1d", focus_size_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 799 | .def("is_trivial_1d", is_trivial_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | .def("shift_origin", shift_origin) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | .def("id", id) - | ~~~~~~~~~~~~~~ - 802 | .def("size", size) - | ~~~~~~~~~~~~~~~~~~ - 803 | .def("__len__", size) - | ~~~~~~~~~~~~~~~~~~~~~ - 804 | .def("__sizeof__", memory_footprint) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 805 | .def("capacity", capacity) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1031 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here - 105 | flex_wrapper::integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = unsigned char]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ - 269 | copy_to_slice(self, slices_simple, other.const_ref()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 289 | setitem_nd_slice(a, slices, b); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 782 | result - | ~~~~~~ - 783 | .def(init const&, optional >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 784 | .def(init >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 785 | .def(init const&>()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 786 | .def("element_size", element_size) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 787 | .staticmethod("element_size") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 788 | .def("accessor", accessor) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 789 | .def("nd", nd) - | ~~~~~~~~~~~~~~ - 790 | .def("is_0_based", is_0_based) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 791 | .def("origin", origin) - | ~~~~~~~~~~~~~~~~~~~~~~ - 792 | .def("all", all) - | ~~~~~~~~~~~~~~~~ - 793 | .def("last", last_0) - | ~~~~~~~~~~~~~~~~~~~~ - 794 | .def("last", last_1) - | ~~~~~~~~~~~~~~~~~~~~ - 795 | .def("is_padded", is_padded) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 796 | .def("focus", focus_0) - | ~~~~~~~~~~~~~~~~~~~~~~ - 797 | .def("focus", focus_1) - | ~~~~~~~~~~~~~~~~~~~~~~ - 798 | .def("focus_size_1d", focus_size_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 799 | .def("is_trivial_1d", is_trivial_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | .def("shift_origin", shift_origin) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | .def("id", id) - | ~~~~~~~~~~~~~~ - 802 | .def("size", size) - | ~~~~~~~~~~~~~~~~~~ - 803 | .def("__len__", size) - | ~~~~~~~~~~~~~~~~~~~~~ - 804 | .def("__sizeof__", memory_footprint) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 805 | .def("capacity", capacity) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 807 | .def("__getitem__", getitem_1d_slice) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1031 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here - 105 | flex_wrapper::integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = short unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 202 | return copy_slice(self, slices_simple); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 782 | result - | ~~~~~~ - 783 | .def(init const&, optional >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 784 | .def(init >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 785 | .def(init const&>()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 786 | .def("element_size", element_size) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 787 | .staticmethod("element_size") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 788 | .def("accessor", accessor) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 789 | .def("nd", nd) - | ~~~~~~~~~~~~~~ - 790 | .def("is_0_based", is_0_based) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 791 | .def("origin", origin) - | ~~~~~~~~~~~~~~~~~~~~~~ - 792 | .def("all", all) - | ~~~~~~~~~~~~~~~~ - 793 | .def("last", last_0) - | ~~~~~~~~~~~~~~~~~~~~ - 794 | .def("last", last_1) - | ~~~~~~~~~~~~~~~~~~~~ - 795 | .def("is_padded", is_padded) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 796 | .def("focus", focus_0) - | ~~~~~~~~~~~~~~~~~~~~~~ - 797 | .def("focus", focus_1) - | ~~~~~~~~~~~~~~~~~~~~~~ - 798 | .def("focus_size_1d", focus_size_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 799 | .def("is_trivial_1d", is_trivial_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | .def("shift_origin", shift_origin) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | .def("id", id) - | ~~~~~~~~~~~~~~ - 802 | .def("size", size) - | ~~~~~~~~~~~~~~~~~~ - 803 | .def("__len__", size) - | ~~~~~~~~~~~~~~~~~~~~~ - 804 | .def("__sizeof__", memory_footprint) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 805 | .def("capacity", capacity) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1031 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here - 105 | flex_wrapper::integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = short unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ - 269 | copy_to_slice(self, slices_simple, other.const_ref()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 289 | setitem_nd_slice(a, slices, b); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 782 | result - | ~~~~~~ - 783 | .def(init const&, optional >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 784 | .def(init >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 785 | .def(init const&>()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 786 | .def("element_size", element_size) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 787 | .staticmethod("element_size") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 788 | .def("accessor", accessor) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 789 | .def("nd", nd) - | ~~~~~~~~~~~~~~ - 790 | .def("is_0_based", is_0_based) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 791 | .def("origin", origin) - | ~~~~~~~~~~~~~~~~~~~~~~ - 792 | .def("all", all) - | ~~~~~~~~~~~~~~~~ - 793 | .def("last", last_0) - | ~~~~~~~~~~~~~~~~~~~~ - 794 | .def("last", last_1) - | ~~~~~~~~~~~~~~~~~~~~ - 795 | .def("is_padded", is_padded) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 796 | .def("focus", focus_0) - | ~~~~~~~~~~~~~~~~~~~~~~ - 797 | .def("focus", focus_1) - | ~~~~~~~~~~~~~~~~~~~~~~ - 798 | .def("focus_size_1d", focus_size_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 799 | .def("is_trivial_1d", is_trivial_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | .def("shift_origin", shift_origin) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | .def("id", id) - | ~~~~~~~~~~~~~~ - 802 | .def("size", size) - | ~~~~~~~~~~~~~~~~~~ - 803 | .def("__len__", size) - | ~~~~~~~~~~~~~~~~~~~~~ - 804 | .def("__sizeof__", memory_footprint) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 805 | .def("capacity", capacity) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 807 | .def("__getitem__", getitem_1d_slice) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1031 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here - 105 | flex_wrapper::integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i >&) [with FloatType = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:119:74: required from here - 119 | double (*matrix_norm_1)(const_ref const &) = matrix::norm_1; - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h:16:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 16 | for (int i=0; i > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 202 | return copy_slice(self, slices_simple); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 782 | result - | ~~~~~~ - 783 | .def(init const&, optional >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 784 | .def(init >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 785 | .def(init const&>()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 786 | .def("element_size", element_size) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 787 | .staticmethod("element_size") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 788 | .def("accessor", accessor) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 789 | .def("nd", nd) - | ~~~~~~~~~~~~~~ - 790 | .def("is_0_based", is_0_based) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 791 | .def("origin", origin) - | ~~~~~~~~~~~~~~~~~~~~~~ - 792 | .def("all", all) - | ~~~~~~~~~~~~~~~~ - 793 | .def("last", last_0) - | ~~~~~~~~~~~~~~~~~~~~ - 794 | .def("last", last_1) - | ~~~~~~~~~~~~~~~~~~~~ - 795 | .def("is_padded", is_padded) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 796 | .def("focus", focus_0) - | ~~~~~~~~~~~~~~~~~~~~~~ - 797 | .def("focus", focus_1) - | ~~~~~~~~~~~~~~~~~~~~~~ - 798 | .def("focus_size_1d", focus_size_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 799 | .def("is_trivial_1d", is_trivial_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | .def("shift_origin", shift_origin) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | .def("id", id) - | ~~~~~~~~~~~~~~ - 802 | .def("size", size) - | ~~~~~~~~~~~~~~~~~~ - 803 | .def("__len__", size) - | ~~~~~~~~~~~~~~~~~~~~~ - 804 | .def("__sizeof__", memory_footprint) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 805 | .def("capacity", capacity) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp: In function ‘scitbx::af::flex::type* scitbx::af::{anonymous}::from_list_or_tuple_of_lists_or_tuples(PyObject*)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:138:38: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 138 | if (PyList_GET_SIZE(row) != n_columns) { + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 154 | if (PyTuple_GET_SIZE(row) != n_columns) { + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:190:38: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 190 | if (PyList_GET_SIZE(row) != n_columns) { + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:206:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 206 | if (PyTuple_GET_SIZE(row) != n_columns) { + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 769 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 770 | shared_plain, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 771 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 772 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ @@ -20990,75 +20674,22 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ - 269 | copy_to_slice(self, slices_simple, other.const_ref()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 289 | setitem_nd_slice(a, slices, b); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 782 | result - | ~~~~~~ - 783 | .def(init const&, optional >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 784 | .def(init >()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 785 | .def(init const&>()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 786 | .def("element_size", element_size) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 787 | .staticmethod("element_size") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 788 | .def("accessor", accessor) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 789 | .def("nd", nd) - | ~~~~~~~~~~~~~~ - 790 | .def("is_0_based", is_0_based) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 791 | .def("origin", origin) - | ~~~~~~~~~~~~~~~~~~~~~~ - 792 | .def("all", all) - | ~~~~~~~~~~~~~~~~ - 793 | .def("last", last_0) - | ~~~~~~~~~~~~~~~~~~~~ - 794 | .def("last", last_1) - | ~~~~~~~~~~~~~~~~~~~~ - 795 | .def("is_padded", is_padded) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 796 | .def("focus", focus_0) - | ~~~~~~~~~~~~~~~~~~~~~~ - 797 | .def("focus", focus_1) - | ~~~~~~~~~~~~~~~~~~~~~~ - 798 | .def("focus_size_1d", focus_size_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 799 | .def("is_trivial_1d", is_trivial_1d) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 800 | .def("shift_origin", shift_origin) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 801 | .def("id", id) - | ~~~~~~~~~~~~~~ - 802 | .def("size", size) - | ~~~~~~~~~~~~~~~~~~ - 803 | .def("__len__", size) - | ~~~~~~~~~~~~~~~~~~~~~ - 804 | .def("__sizeof__", memory_footprint) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 805 | .def("capacity", capacity) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 807 | .def("__getitem__", getitem_1d_slice) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 773 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 774 | shared, + | ~~~~~~~~~~~~~~~~~~~~ + 775 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 776 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ @@ -21071,167 +20702,33 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i >&) [with FloatType = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:177:11: required from here - 145 | class_f_t - | ~~~~~~~~~ - 146 | .def("is_square_matrix", is_square_matrix) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 147 | .def("matrix_diagonal", - | ~~~~~~~~~~~~~~~~~~~~~~~ - 148 | (shared(*)( - | ~~~~~~~~~~~~~~~~~~~ - 149 | const_ref > const&)) matrix_diagonal) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 150 | .def("matrix_upper_bidiagonal", matrix_upper_bidiagonal) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 151 | .def("matrix_lower_bidiagonal", matrix_lower_bidiagonal) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 152 | .def("matrix_diagonal_set_in_place", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 153 | (void(*)( - | ~~~~~~~~~ - 154 | ref > const&, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 155 | double const&)) matrix_diagonal_set_in_place, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 156 | arg("value")) - | ~~~~~~~~~~~~~ - 157 | .def("matrix_diagonal_set_in_place", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 158 | (void(*)( - | ~~~~~~~~~ - 159 | ref > const&, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 160 | const_ref const&)) matrix_diagonal_set_in_place, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 161 | arg("diagonal")) - | ~~~~~~~~~~~~~~~~ - 162 | .def("matrix_diagonal_add_in_place", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 163 | (void(*)( - | ~~~~~~~~~ - 164 | ref > const&, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 165 | double const&)) matrix_diagonal_add_in_place, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 166 | arg("value")) - | ~~~~~~~~~~~~~ - 167 | .def("matrix_diagonal_sum", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 168 | (double(*)( - | ~~~~~~~~~~~ - 169 | const_ref > const&)) matrix_diagonal_sum) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 170 | .def("matrix_trace", - | ~~~~~~~~~~~~~~~~~~~~ - 171 | (double(*)( - | ~~~~~~~~~~~ - 172 | const_ref > const&)) matrix_diagonal_sum) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 173 | .def("matrix_diagonal_product", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 174 | (double(*)( - | ~~~~~~~~~~~ - 175 | const_ref > const&)) matrix_diagonal_product) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 176 | .def("matrix_norm_1", matrix_norm_1) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 177 | .def("matrix_norm_inf", matrix::norm_inf) - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h:32:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 32 | for (int i=0; i >&) [with FloatType = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double_matrix.cpp:178:11: required from here - 145 | class_f_t - | ~~~~~~~~~ - 146 | .def("is_square_matrix", is_square_matrix) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 147 | .def("matrix_diagonal", - | ~~~~~~~~~~~~~~~~~~~~~~~ - 148 | (shared(*)( - | ~~~~~~~~~~~~~~~~~~~ - 149 | const_ref > const&)) matrix_diagonal) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 150 | .def("matrix_upper_bidiagonal", matrix_upper_bidiagonal) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 151 | .def("matrix_lower_bidiagonal", matrix_lower_bidiagonal) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 152 | .def("matrix_diagonal_set_in_place", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 153 | (void(*)( - | ~~~~~~~~~ - 154 | ref > const&, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 155 | double const&)) matrix_diagonal_set_in_place, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 156 | arg("value")) - | ~~~~~~~~~~~~~ - 157 | .def("matrix_diagonal_set_in_place", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 158 | (void(*)( - | ~~~~~~~~~ - 159 | ref > const&, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 160 | const_ref const&)) matrix_diagonal_set_in_place, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 161 | arg("diagonal")) - | ~~~~~~~~~~~~~~~~ - 162 | .def("matrix_diagonal_add_in_place", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 163 | (void(*)( - | ~~~~~~~~~ - 164 | ref > const&, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 165 | double const&)) matrix_diagonal_add_in_place, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 166 | arg("value")) - | ~~~~~~~~~~~~~ - 167 | .def("matrix_diagonal_sum", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 168 | (double(*)( - | ~~~~~~~~~~~ - 169 | const_ref > const&)) matrix_diagonal_sum) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 170 | .def("matrix_trace", - | ~~~~~~~~~~~~~~~~~~~~ - 171 | (double(*)( - | ~~~~~~~~~~~ - 172 | const_ref > const&)) matrix_diagonal_sum) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 173 | .def("matrix_diagonal_product", - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 174 | (double(*)( - | ~~~~~~~~~~~ - 175 | const_ref > const&)) matrix_diagonal_product) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 176 | .def("matrix_norm_1", matrix_norm_1) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 177 | .def("matrix_norm_inf", matrix::norm_inf) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 178 | .def("matrix_norm_frobenius", matrix::norm_frobenius) - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h:46:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 46 | for (int k=0; k < a_ij.size(); ++k) norm_accu(a_ij[k]); - | ~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = long unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = long unsigned int]’ - 119 | detail::copy_to_slice_detail(self, slices, other); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ - 269 | copy_to_slice(self, slices_simple, other.const_ref()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 289 | setitem_nd_slice(a, slices, b); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp: In function ‘std::string scitbx::af::{anonymous}::mathematica_form(const scitbx::af::const_ref >&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:452:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::small_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 452 | for (int i=1; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 454 | if (i != indices.size() - 1) o << ","; + | ~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:7: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h: In instantiation of ‘FloatType scitbx::matrix::norm_1(const scitbx::af::const_ref&) [with FloatType = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:365:26: required from here + 365 | return matrix::norm_1(self); + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h:25:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 25 | for (int i=0; i > scitbx::af::copy_slice(const const_ref >&, small) [with T = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 202 | return copy_slice(self, slices_simple); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -21281,14 +20778,6 @@ 805 | .def("capacity", capacity) | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 807 | .def("__getitem__", getitem_1d_slice) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) @@ -21302,71 +20791,17 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 70 | if (idx_a[j] < slices[j].stop) break; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::first_index_a_s(const f_t&, e_t) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:963:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 963 | def("first_index", first_index_a_s); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1031 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1048:21: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::signed_integer(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1048 | return integer(python_name, flex_root_scope); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here - 242 | flex_wrapper::signed_integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_function.h:1441, - from /usr/include/c++/15/functional:51, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:15, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/to_python_value.hpp:14, - from /usr/include/boost/python/default_call_policies.hpp:10, - from /usr/include/boost/python/make_function.hpp:10, - from /usr/include/boost/python/def.hpp:11, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/15/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::last_index_a_s(const f_t&, e_t) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:964:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 964 | def("last_index", last_index_a_s); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1031 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1048:21: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::signed_integer(const std::string&, const boost::python::api::object&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1048 | return integer(python_name, flex_root_scope); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_int.cpp:319:3: required from here - 242 | flex_wrapper::signed_integer(#pyname, scope()) \ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = unsigned char]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = unsigned char]’ - 119 | detail::copy_to_slice_detail(self, slices, other); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 289 | setitem_nd_slice(a, slices, b); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -21425,51 +20860,47 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 70 | if (idx_a[j] < slices[j].stop) break; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp: In function ‘scitbx::af::flex::type* scitbx::af::{anonymous}::from_list_or_tuple_of_lists_or_tuples(PyObject*)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:138:38: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 138 | if (PyList_GET_SIZE(row) != n_columns) { - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:154:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 154 | if (PyTuple_GET_SIZE(row) != n_columns) { - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:190:38: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 190 | if (PyList_GET_SIZE(row) != n_columns) { - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:206:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 206 | if (PyTuple_GET_SIZE(row) != n_columns) { - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp: In function ‘std::string scitbx::af::{anonymous}::mathematica_form(const scitbx::af::const_ref >&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:452:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::small_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 452 | for (int i=1; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 454 | if (i != indices.size() - 1) o << ","; - | ~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = short unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = short unsigned int]’ - 119 | detail::copy_to_slice_detail(self, slices, other); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ - 269 | copy_to_slice(self, slices_simple, other.const_ref()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 289 | setitem_nd_slice(a, slices, b); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 114 | for (int i=0;i scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:536:8: required from here + 536 | def( + | ~~~^ + 537 | "double_from_byte_str", + | ~~~~~~~~~~~~~~~~~~~~~~~ + 538 | shared_from_byte_str, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 539 | (arg("byte_str"))); + | ~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ + 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); + | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned char]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 202 | return copy_slice(self, slices_simple); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -21519,48 +20950,30 @@ 805 | .def("capacity", capacity) | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 807 | .def("__getitem__", getitem_1d_slice) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 70 | if (idx_a[j] < slices[j].stop) break; -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h: In instantiation of ‘FloatType scitbx::matrix::norm_1(const scitbx::af::const_ref&) [with FloatType = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:365:26: required from here - 365 | return matrix::norm_1(self); - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/norms.h:25:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 25 | for (int i=0; i >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = unsigned int]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = unsigned int]’ - 119 | detail::copy_to_slice_detail(self, slices, other); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = unsigned char]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 289 | setitem_nd_slice(a, slices, b); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -21619,165 +21032,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here 105 | flex_wrapper::integer(#pyname, scope()) \ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 70 | if (idx_a[j] < slices[j].stop) break; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h: In instantiation of ‘scitbx::af::shared scitbx::af::boost_python::shared_from_byte_str(const boost::python::api::object&) [with ElementType = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:536:8: required from here - 536 | def( - | ~~~^ - 537 | "double_from_byte_str", - | ~~~~~~~~~~~~~~~~~~~~~~~ - 538 | shared_from_byte_str, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 539 | (arg("byte_str"))); - | ~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘boost::python::ssize_t’ {aka ‘long int’} [-Wsign-compare] - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/byte_str.h:81:5: note: in expansion of macro ‘SCITBX_ASSERT’ - 81 | SCITBX_ASSERT(shared_array_size * sizeof(ElementType) == len_byte_str); - | ^~~~~~~~~~~~~ -g++ -o lib/mmtbx_tls_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_tls_utils_ext.so.0 mmtbx/tls/utils.o mmtbx/tls/utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::first_index_a_s(const f_t&, e_t) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:963:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 963 | def("first_index", first_index_a_s); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1020 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here - 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:616:41: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_function.h:1441, - from /usr/include/c++/15/functional:51, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:15, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/to_python_value.hpp:14, - from /usr/include/boost/python/default_call_policies.hpp:10, - from /usr/include/boost/python/make_function.hpp:10, - from /usr/include/boost/python/def.hpp:11, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/15/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::last_index_a_s(const f_t&, e_t) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:964:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 964 | def("last_index", last_index_a_s); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1020 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here - 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ -Create symlinks for: 'lib/mmtbx_tls_utils_ext.so.0.0.1' - 'lib/mmtbx_tls_utils_ext.so.0'->'lib/mmtbx_tls_utils_ext.so.0.0.1' - 'lib/mmtbx_tls_utils_ext.so'->'lib/mmtbx_tls_utils_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_std_string.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_std_string.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /usr/include/c++/15/cassert:46, - from /usr/include/boost/move/detail/type_traits.hpp:33, - from /usr/include/boost/move/traits.hpp:31, - from /usr/include/boost/move/utility.hpp:30, - from /usr/include/boost/optional/optional.hpp:59, - from /usr/include/boost/optional.hpp:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref_reductions.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 769 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 770 | shared_plain, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 771 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 772 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1020 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here - 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 773 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 774 | shared, - | ~~~~~~~~~~~~~~~~~~~~ - 775 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 776 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 910 | return plain(python_name) - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 966 | return numeric_common(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1020 | return numeric_no_pow(python_name, flex_root_scope) - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here - 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 114 | for (int i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = short unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 202 | return copy_slice(self, slices_simple); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -21910,29 +21178,29 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1020 | return numeric_no_pow(python_name, flex_root_scope) +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here - 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here + 105 | flex_wrapper::integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for (int i=0;i >&, small, const const_ref >&) [with T = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = short unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 289 | setitem_nd_slice(a, slices, b); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -21991,21 +21259,221 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1031 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here + 105 | flex_wrapper::integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 114 | for (int i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 202 | return copy_slice(self, slices_simple); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 782 | result + | ~~~~~~ + 783 | .def(init const&, optional >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 784 | .def(init >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 785 | .def(init const&>()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 786 | .def("element_size", element_size) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 787 | .staticmethod("element_size") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 788 | .def("accessor", accessor) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 789 | .def("nd", nd) + | ~~~~~~~~~~~~~~ + 790 | .def("is_0_based", is_0_based) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 791 | .def("origin", origin) + | ~~~~~~~~~~~~~~~~~~~~~~ + 792 | .def("all", all) + | ~~~~~~~~~~~~~~~~ + 793 | .def("last", last_0) + | ~~~~~~~~~~~~~~~~~~~~ + 794 | .def("last", last_1) + | ~~~~~~~~~~~~~~~~~~~~ + 795 | .def("is_padded", is_padded) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 796 | .def("focus", focus_0) + | ~~~~~~~~~~~~~~~~~~~~~~ + 797 | .def("focus", focus_1) + | ~~~~~~~~~~~~~~~~~~~~~~ + 798 | .def("focus_size_1d", focus_size_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 799 | .def("is_trivial_1d", is_trivial_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | .def("shift_origin", shift_origin) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | .def("id", id) + | ~~~~~~~~~~~~~~ + 802 | .def("size", size) + | ~~~~~~~~~~~~~~~~~~ + 803 | .def("__len__", size) + | ~~~~~~~~~~~~~~~~~~~~~ + 804 | .def("__sizeof__", memory_footprint) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 805 | .def("capacity", capacity) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1031 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here + 105 | flex_wrapper::integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ + 269 | copy_to_slice(self, slices_simple, other.const_ref()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 289 | setitem_nd_slice(a, slices, b); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 782 | result + | ~~~~~~ + 783 | .def(init const&, optional >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 784 | .def(init >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 785 | .def(init const&>()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 786 | .def("element_size", element_size) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 787 | .staticmethod("element_size") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 788 | .def("accessor", accessor) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 789 | .def("nd", nd) + | ~~~~~~~~~~~~~~ + 790 | .def("is_0_based", is_0_based) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 791 | .def("origin", origin) + | ~~~~~~~~~~~~~~~~~~~~~~ + 792 | .def("all", all) + | ~~~~~~~~~~~~~~~~ + 793 | .def("last", last_0) + | ~~~~~~~~~~~~~~~~~~~~ + 794 | .def("last", last_1) + | ~~~~~~~~~~~~~~~~~~~~ + 795 | .def("is_padded", is_padded) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 796 | .def("focus", focus_0) + | ~~~~~~~~~~~~~~~~~~~~~~ + 797 | .def("focus", focus_1) + | ~~~~~~~~~~~~~~~~~~~~~~ + 798 | .def("focus_size_1d", focus_size_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 799 | .def("is_trivial_1d", is_trivial_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | .def("shift_origin", shift_origin) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | .def("id", id) + | ~~~~~~~~~~~~~~ + 802 | .def("size", size) + | ~~~~~~~~~~~~~~~~~~ + 803 | .def("__len__", size) + | ~~~~~~~~~~~~~~~~~~~~~ + 804 | .def("__sizeof__", memory_footprint) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 805 | .def("capacity", capacity) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 807 | .def("__getitem__", getitem_1d_slice) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1031 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here + 105 | flex_wrapper::integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 114 | for (int i=0;i scitbx::af::boost_python::flex_wrapper::first_index_a_s(const f_t&, e_t) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:963:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 963 | def("first_index", first_index_a_s); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 1020 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 616 | return first_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_function.h:1441, + from /usr/include/c++/15/functional:51, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:15, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/to_python_value.hpp:14, + from /usr/include/boost/python/default_call_policies.hpp:10, + from /usr/include/boost/python/make_function.hpp:10, + from /usr/include/boost/python/def.hpp:11, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: +/usr/include/c++/15/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h: In instantiation of ‘static boost::optional scitbx::af::boost_python::flex_wrapper::last_index_a_s(const f_t&, e_t) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >; e_t = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:964:12: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 964 | def("last_index", last_index_a_s); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1020 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here + 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:621:40: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 621 | return last_index(a, std::bind2nd(std::equal_to(), x)); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, @@ -22068,17 +21536,17 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = double]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = double]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = long unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = long unsigned int]’ 119 | detail::copy_to_slice_detail(self, slices, other); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 289 | setitem_nd_slice(a, slices, b); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -22137,18 +21605,18 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 910 | return plain(python_name) | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 966 | return numeric_common(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 1020 | return numeric_no_pow(python_name, flex_root_scope) +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = long unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1031 | return numeric_no_pow(python_name, flex_root_scope) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here - 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:140:3: required from here + 105 | flex_wrapper::integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: @@ -22213,6 +21681,89 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = unsigned char]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = unsigned char]’ + 119 | detail::copy_to_slice_detail(self, slices, other); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ + 269 | copy_to_slice(self, slices_simple, other.const_ref()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 289 | setitem_nd_slice(a, slices, b); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 782 | result + | ~~~~~~ + 783 | .def(init const&, optional >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 784 | .def(init >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 785 | .def(init const&>()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 786 | .def("element_size", element_size) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 787 | .staticmethod("element_size") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 788 | .def("accessor", accessor) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 789 | .def("nd", nd) + | ~~~~~~~~~~~~~~ + 790 | .def("is_0_based", is_0_based) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 791 | .def("origin", origin) + | ~~~~~~~~~~~~~~~~~~~~~~ + 792 | .def("all", all) + | ~~~~~~~~~~~~~~~~ + 793 | .def("last", last_0) + | ~~~~~~~~~~~~~~~~~~~~ + 794 | .def("last", last_1) + | ~~~~~~~~~~~~~~~~~~~~ + 795 | .def("is_padded", is_padded) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 796 | .def("focus", focus_0) + | ~~~~~~~~~~~~~~~~~~~~~~ + 797 | .def("focus", focus_1) + | ~~~~~~~~~~~~~~~~~~~~~~ + 798 | .def("focus_size_1d", focus_size_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 799 | .def("is_trivial_1d", is_trivial_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | .def("shift_origin", shift_origin) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | .def("id", id) + | ~~~~~~~~~~~~~~ + 802 | .def("size", size) + | ~~~~~~~~~~~~~~~~~~ + 803 | .def("__len__", size) + | ~~~~~~~~~~~~~~~~~~~~~ + 804 | .def("__sizeof__", memory_footprint) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 805 | .def("capacity", capacity) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 807 | .def("__getitem__", getitem_1d_slice) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned char; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1031 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:141:3: required from here + 105 | flex_wrapper::integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 70 | if (idx_a[j] < slices[j].stop) break; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, @@ -22275,6 +21826,172 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = short unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = short unsigned int]’ + 119 | detail::copy_to_slice_detail(self, slices, other); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ + 269 | copy_to_slice(self, slices_simple, other.const_ref()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 289 | setitem_nd_slice(a, slices, b); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 782 | result + | ~~~~~~ + 783 | .def(init const&, optional >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 784 | .def(init >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 785 | .def(init const&>()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 786 | .def("element_size", element_size) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 787 | .staticmethod("element_size") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 788 | .def("accessor", accessor) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 789 | .def("nd", nd) + | ~~~~~~~~~~~~~~ + 790 | .def("is_0_based", is_0_based) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 791 | .def("origin", origin) + | ~~~~~~~~~~~~~~~~~~~~~~ + 792 | .def("all", all) + | ~~~~~~~~~~~~~~~~ + 793 | .def("last", last_0) + | ~~~~~~~~~~~~~~~~~~~~ + 794 | .def("last", last_1) + | ~~~~~~~~~~~~~~~~~~~~ + 795 | .def("is_padded", is_padded) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 796 | .def("focus", focus_0) + | ~~~~~~~~~~~~~~~~~~~~~~ + 797 | .def("focus", focus_1) + | ~~~~~~~~~~~~~~~~~~~~~~ + 798 | .def("focus_size_1d", focus_size_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 799 | .def("is_trivial_1d", is_trivial_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | .def("shift_origin", shift_origin) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | .def("id", id) + | ~~~~~~~~~~~~~~ + 802 | .def("size", size) + | ~~~~~~~~~~~~~~~~~~ + 803 | .def("__len__", size) + | ~~~~~~~~~~~~~~~~~~~~~ + 804 | .def("__sizeof__", memory_footprint) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 805 | .def("capacity", capacity) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 807 | .def("__getitem__", getitem_1d_slice) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = short unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1031 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:142:3: required from here + 105 | flex_wrapper::integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 70 | if (idx_a[j] < slices[j].stop) break; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = unsigned int]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = unsigned int]’ + 119 | detail::copy_to_slice_detail(self, slices, other); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ + 269 | copy_to_slice(self, slices_simple, other.const_ref()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 289 | setitem_nd_slice(a, slices, b); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 782 | result + | ~~~~~~ + 783 | .def(init const&, optional >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 784 | .def(init >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 785 | .def(init const&>()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 786 | .def("element_size", element_size) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 787 | .staticmethod("element_size") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 788 | .def("accessor", accessor) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 789 | .def("nd", nd) + | ~~~~~~~~~~~~~~ + 790 | .def("is_0_based", is_0_based) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 791 | .def("origin", origin) + | ~~~~~~~~~~~~~~~~~~~~~~ + 792 | .def("all", all) + | ~~~~~~~~~~~~~~~~ + 793 | .def("last", last_0) + | ~~~~~~~~~~~~~~~~~~~~ + 794 | .def("last", last_1) + | ~~~~~~~~~~~~~~~~~~~~ + 795 | .def("is_padded", is_padded) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 796 | .def("focus", focus_0) + | ~~~~~~~~~~~~~~~~~~~~~~ + 797 | .def("focus", focus_1) + | ~~~~~~~~~~~~~~~~~~~~~~ + 798 | .def("focus_size_1d", focus_size_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 799 | .def("is_trivial_1d", is_trivial_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | .def("shift_origin", shift_origin) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | .def("id", id) + | ~~~~~~~~~~~~~~ + 802 | .def("size", size) + | ~~~~~~~~~~~~~~~~~~ + 803 | .def("__len__", size) + | ~~~~~~~~~~~~~~~~~~~~~ + 804 | .def("__sizeof__", memory_footprint) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 805 | .def("capacity", capacity) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 807 | .def("__getitem__", getitem_1d_slice) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1031:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::integer(const std::string&, const boost::python::api::object&) [with ElementType = unsigned int; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1031 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_size_t.cpp:143:3: required from here + 105 | flex_wrapper::integer(#pyname, scope()) \ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 70 | if (idx_a[j] < slices[j].stop) break; In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -22436,6 +22153,73 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | for (int i=0;i::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 769 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 770 | shared_plain, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 771 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 772 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1020 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here + 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 773 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 774 | shared, + | ~~~~~~~~~~~~~~~~~~~~ + 775 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 776 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1020 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here + 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = long int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = long int; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 202 | return copy_slice(self, slices_simple); @@ -22916,6 +22700,161 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | for (int i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 202 | return copy_slice(self, slices_simple); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 782 | result + | ~~~~~~ + 783 | .def(init const&, optional >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 784 | .def(init >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 785 | .def(init const&>()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 786 | .def("element_size", element_size) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 787 | .staticmethod("element_size") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 788 | .def("accessor", accessor) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 789 | .def("nd", nd) + | ~~~~~~~~~~~~~~ + 790 | .def("is_0_based", is_0_based) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 791 | .def("origin", origin) + | ~~~~~~~~~~~~~~~~~~~~~~ + 792 | .def("all", all) + | ~~~~~~~~~~~~~~~~ + 793 | .def("last", last_0) + | ~~~~~~~~~~~~~~~~~~~~ + 794 | .def("last", last_1) + | ~~~~~~~~~~~~~~~~~~~~ + 795 | .def("is_padded", is_padded) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 796 | .def("focus", focus_0) + | ~~~~~~~~~~~~~~~~~~~~~~ + 797 | .def("focus", focus_1) + | ~~~~~~~~~~~~~~~~~~~~~~ + 798 | .def("focus_size_1d", focus_size_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 799 | .def("is_trivial_1d", is_trivial_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | .def("shift_origin", shift_origin) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | .def("id", id) + | ~~~~~~~~~~~~~~ + 802 | .def("size", size) + | ~~~~~~~~~~~~~~~~~~ + 803 | .def("__len__", size) + | ~~~~~~~~~~~~~~~~~~~~~ + 804 | .def("__sizeof__", memory_footprint) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 805 | .def("capacity", capacity) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1020 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here + 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ + 269 | copy_to_slice(self, slices_simple, other.const_ref()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 289 | setitem_nd_slice(a, slices, b); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 782 | result + | ~~~~~~ + 783 | .def(init const&, optional >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 784 | .def(init >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 785 | .def(init const&>()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 786 | .def("element_size", element_size) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 787 | .staticmethod("element_size") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 788 | .def("accessor", accessor) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 789 | .def("nd", nd) + | ~~~~~~~~~~~~~~ + 790 | .def("is_0_based", is_0_based) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 791 | .def("origin", origin) + | ~~~~~~~~~~~~~~~~~~~~~~ + 792 | .def("all", all) + | ~~~~~~~~~~~~~~~~ + 793 | .def("last", last_0) + | ~~~~~~~~~~~~~~~~~~~~ + 794 | .def("last", last_1) + | ~~~~~~~~~~~~~~~~~~~~ + 795 | .def("is_padded", is_padded) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 796 | .def("focus", focus_0) + | ~~~~~~~~~~~~~~~~~~~~~~ + 797 | .def("focus", focus_1) + | ~~~~~~~~~~~~~~~~~~~~~~ + 798 | .def("focus_size_1d", focus_size_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 799 | .def("is_trivial_1d", is_trivial_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | .def("shift_origin", shift_origin) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | .def("id", id) + | ~~~~~~~~~~~~~~ + 802 | .def("size", size) + | ~~~~~~~~~~~~~~~~~~ + 803 | .def("__len__", size) + | ~~~~~~~~~~~~~~~~~~~~~ + 804 | .def("__sizeof__", memory_footprint) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 805 | .def("capacity", capacity) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 807 | .def("__getitem__", getitem_1d_slice) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1020 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here + 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 114 | for (int i=0;i >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = int]’ 119 | detail::copy_to_slice_detail(self, slices, other); @@ -23002,21 +22941,89 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:1: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = double]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = double]’ + 119 | detail::copy_to_slice_detail(self, slices, other); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa >]’ + 269 | copy_to_slice(self, slices_simple, other.const_ref()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 289 | setitem_nd_slice(a, slices, b); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 782 | result + | ~~~~~~ + 783 | .def(init const&, optional >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 784 | .def(init >()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 785 | .def(init const&>()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 786 | .def("element_size", element_size) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 787 | .staticmethod("element_size") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 788 | .def("accessor", accessor) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 789 | .def("nd", nd) + | ~~~~~~~~~~~~~~ + 790 | .def("is_0_based", is_0_based) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 791 | .def("origin", origin) + | ~~~~~~~~~~~~~~~~~~~~~~ + 792 | .def("all", all) + | ~~~~~~~~~~~~~~~~ + 793 | .def("last", last_0) + | ~~~~~~~~~~~~~~~~~~~~ + 794 | .def("last", last_1) + | ~~~~~~~~~~~~~~~~~~~~ + 795 | .def("is_padded", is_padded) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 796 | .def("focus", focus_0) + | ~~~~~~~~~~~~~~~~~~~~~~ + 797 | .def("focus", focus_1) + | ~~~~~~~~~~~~~~~~~~~~~~ + 798 | .def("focus_size_1d", focus_size_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 799 | .def("is_trivial_1d", is_trivial_1d) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 800 | .def("shift_origin", shift_origin) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 801 | .def("id", id) + | ~~~~~~~~~~~~~~ + 802 | .def("size", size) + | ~~~~~~~~~~~~~~~~~~ + 803 | .def("__len__", size) + | ~~~~~~~~~~~~~~~~~~~~~ + 804 | .def("__sizeof__", memory_footprint) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 805 | .def("capacity", capacity) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 807 | .def("__getitem__", getitem_1d_slice) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:910:19: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_common(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 910 | return plain(python_name) + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:966:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric_no_pow(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 966 | return numeric_common(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:1020:28: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::numeric(const std::string&, const boost::python::api::object&) [with ElementType = double; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_ >, scitbx::af::boost_python::flex_wrapper, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 1020 | return numeric_no_pow(python_name, flex_root_scope) + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_double.cpp:477:42: required from here + 477 | f_w::class_f_t class_f_t(f_w::numeric("double", scope())); + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 70 | if (idx_a[j] < slices[j].stop) break; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = long int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = long int]’ 119 | detail::copy_to_slice_detail(self, slices, other); @@ -23189,6 +23196,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_complex_double.cpp:1: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ^~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = short int]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = short int]’ 119 | detail::copy_to_slice_detail(self, slices, other); @@ -23550,8 +23572,37 @@ | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; +g++ -o lib/mmtbx_tls_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=mmtbx_tls_utils_ext.so.0 mmtbx/tls/utils.o mmtbx/tls/utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lmmtbx_tls -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/mmtbx_tls_utils_ext.so.0.0.1' + 'lib/mmtbx_tls_utils_ext.so.0'->'lib/mmtbx_tls_utils_ext.so.0.0.1' + 'lib/mmtbx_tls_utils_ext.so'->'lib/mmtbx_tls_utils_ext.so.0.0.1' +g++ -o scitbx/array_family/boost_python/flex_std_string.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_std_string.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/array_family/boost_python/flex_random.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_random.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/rstbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_ext.so.0 rstbx/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/rstbx_ext.so.0.0.1' + 'lib/rstbx_ext.so.0'->'lib/rstbx_ext.so.0.0.1' + 'lib/rstbx_ext.so'->'lib/rstbx_ext.so.0.0.1' +g++ -o scitbx/array_family/boost_python/flex_sort.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sort.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_std_string.cpp:3: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h: In function ‘scitbx::af::shared > scitbx::misc::split_lines(const char*, std::size_t, bool, bool)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/misc/split_lines.h:24:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] @@ -23887,21 +23938,6 @@ | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; -g++ -o lib/rstbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_ext.so.0 rstbx/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/rstbx_ext.so.0.0.1' - 'lib/rstbx_ext.so.0'->'lib/rstbx_ext.so.0.0.1' - 'lib/rstbx_ext.so'->'lib/rstbx_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/flex_sort.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sort.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/rstbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=rstbx_array_family_flex_ext.so.0 rstbx/array_family/ext.o rstbx/array_family/flex_rstbx_arrays.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lrstbx -lann-cctbx -lcctbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libann-cctbx.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -23953,6 +23989,12 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/array_family/boost_python/flex_vec3_int.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_vec3_int.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/array_family/boost_python/flex_sym_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/array_family/boost_python/flex_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/array_family/boost_python/flex_tiny_size_t_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, @@ -23968,10 +24010,21 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); | ^~~~~~~~~~~~~ -g++ -o scitbx/array_family/boost_python/flex_sym_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/array_family/boost_python/flex_mat3_double.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:3: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ^~~~~~~~~~~~~ In file included from /usr/include/c++/15/cassert:46, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -24002,6 +24055,11 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp: In function ‘scitbx::af::flex >::type* scitbx::af::{anonymous}::array_indices_as_double_from_array_focus_dimensions(const scitbx::vec2&)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:128:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] + 128 | for(std::size_t i=0;i::convertible(PyObject*) [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, @@ -24021,24 +24079,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:3: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp: In function ‘scitbx::af::flex >::type* scitbx::af::{anonymous}::array_indices_as_double_from_array_focus_dimensions(const scitbx::vec2&)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_vec2_double.cpp:128:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] - 128 | for(std::size_t i=0;i > scitbx::af::copy_slice(const const_ref >&, small) [with T = scitbx::vec3]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::vec3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -24104,8 +24144,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for (int i=0;i >&, small, const const_ref >&) [with T = scitbx::vec3]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::vec3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); @@ -24301,8 +24339,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -g++ -o scitbx/array_family/boost_python/flex_tiny_size_t_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = scitbx::vec2]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::vec2; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -24440,8 +24476,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | for (int i=0;i >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = scitbx::vec2]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = scitbx::vec2]’ 119 | detail::copy_to_slice_detail(self, slices, other); @@ -24516,8 +24550,6 @@ | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; -g++ -o scitbx/array_family/boost_python/show_sizes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/show_sizes.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, @@ -24533,21 +24565,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:3: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ^~~~~~~~~~~~~ +g++ -o scitbx/array_family/boost_python/loops.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/loops.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/c++/15/cassert:46, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -24597,21 +24616,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:3: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ - 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); - | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = scitbx::vec3]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::vec3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ @@ -24749,55 +24753,21 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | for (int i=0;i::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 769 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 770 | shared_plain, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 771 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 772 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here - 180 | f_w::plain("mat3_double") - | ~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 773 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 774 | shared, - | ~~~~~~~~~~~~~~~~~~~~ - 775 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 776 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here - 180 | f_w::plain("mat3_double") - | ~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:3: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ^~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = scitbx::vec3]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = scitbx::vec3]’ 119 | detail::copy_to_slice_detail(self, slices, other); @@ -24872,15 +24842,79 @@ | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; +In file included from /usr/include/c++/15/cassert:46, + from /usr/include/boost/move/detail/type_traits.hpp:33, + from /usr/include/boost/move/traits.hpp:31, + from /usr/include/boost/move/utility.hpp:30, + from /usr/include/boost/optional/optional.hpp:59, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 769 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 770 | shared_plain, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 771 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 772 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here + 124 | f_w::plain("sym_mat3_double") + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 773 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 774 | shared, + | ~~~~~~~~~~~~~~~~~~~~ + 775 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 776 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here + 124 | f_w::plain("sym_mat3_double") + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:3: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h: In member function ‘void scitbx::af::boost_python::detail::getstate_manager::advance(char*)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:43: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_pickle_single_buffered.h:43:9: note: in expansion of macro ‘SCITBX_ASSERT’ + 43 | SCITBX_ASSERT(str_end - str_begin <= str_capacity); + | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = scitbx::mat3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = scitbx::sym_mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 202 | return copy_slice(self, slices_simple); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -24931,20 +24965,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here - 180 | f_w::plain("mat3_double") - | ~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here + 124 | f_w::plain("sym_mat3_double") + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for (int i=0;i >&, small, const const_ref >&) [with T = scitbx::mat3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = scitbx::sym_mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 289 | setitem_nd_slice(a, slices, b); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -25003,72 +25037,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here - 180 | f_w::plain("mat3_double") - | ~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 769 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 770 | shared_plain, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 771 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 772 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here - 124 | f_w::plain("sym_mat3_double") - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 773 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 774 | shared, - | ~~~~~~~~~~~~~~~~~~~~ - 775 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 776 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here 124 | f_w::plain("sym_mat3_double") | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = scitbx::mat3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = scitbx::mat3]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 114 | for (int i=0;i >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = scitbx::sym_mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = scitbx::sym_mat3]’ 119 | detail::copy_to_slice_detail(self, slices, other); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 289 | setitem_nd_slice(a, slices, b); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -25127,20 +25114,121 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here + 124 | f_w::plain("sym_mat3_double") + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 70 | if (idx_a[j] < slices[j].stop) break; +In file included from /usr/include/c++/15/cassert:46, + from /usr/include/boost/move/detail/type_traits.hpp:33, + from /usr/include/boost/move/traits.hpp:31, + from /usr/include/boost/move/utility.hpp:30, + from /usr/include/boost/optional/optional.hpp:59, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 769 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 770 | shared_plain, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 771 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 772 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here 180 | f_w::plain("mat3_double") | ~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 70 | if (idx_a[j] < slices[j].stop) break; +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 773 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 774 | shared, + | ~~~~~~~~~~~~~~~~~~~~ + 775 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 776 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here + 180 | f_w::plain("mat3_double") + | ~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +In file included from /usr/include/c++/15/cassert:46, + from /usr/include/boost/move/detail/type_traits.hpp:33, + from /usr/include/boost/move/traits.hpp:31, + from /usr/include/boost/move/utility.hpp:30, + from /usr/include/boost/optional/optional.hpp:59, + from /usr/include/boost/optional.hpp:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref_reductions.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:3: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 769 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 770 | shared_plain, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ + 771 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 772 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:32:47: required from here + 32 | flex_wrapper >::plain("tiny_size_t_2") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ + 773 | scitbx::boost_python::container_conversions::from_python_sequence< + | ^~~~~~~~~~~~~~~~~~~~~ + 774 | shared, + | ~~~~~~~~~~~~~~~~~~~~ + 775 | scitbx::boost_python::container_conversions + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 776 | ::variable_capacity_policy>(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:32:47: required from here + 32 | flex_wrapper >::plain("tiny_size_t_2") + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = scitbx::sym_mat3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = scitbx::mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 202 | return copy_slice(self, slices_simple); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -25191,20 +25279,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here - 124 | f_w::plain("sym_mat3_double") - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here + 180 | f_w::plain("mat3_double") + | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 89 | for (int i=0;i >&, small, const const_ref >&) [with T = scitbx::sym_mat3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = scitbx::mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 289 | setitem_nd_slice(a, slices, b); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -25263,23 +25351,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here - 124 | f_w::plain("sym_mat3_double") - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_mat3_double.cpp:180:15: required from here + 180 | f_w::plain("mat3_double") + | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 114 | for (int i=0;i >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = scitbx::sym_mat3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = scitbx::sym_mat3]’ - 119 | detail::copy_to_slice_detail(self, slices, other); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ - 269 | copy_to_slice(self, slices_simple, other.const_ref()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 289 | setitem_nd_slice(a, slices, b); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::sym_mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = tiny]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 202 | return copy_slice(self, slices_simple); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -25329,83 +25415,21 @@ 805 | .def("capacity", capacity) | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 807 | .def("__getitem__", getitem_1d_slice) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_sym_mat3_double.cpp:124:15: required from here - 124 | f_w::plain("sym_mat3_double") - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 70 | if (idx_a[j] < slices[j].stop) break; -g++ -o scitbx/array_family/boost_python/numpy_bridge.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DSCITBX_HAVE_NUMPY_INCLUDE -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /usr/include/c++/15/cassert:46, - from /usr/include/boost/move/detail/type_traits.hpp:33, - from /usr/include/boost/move/traits.hpp:31, - from /usr/include/boost/move/utility.hpp:30, - from /usr/include/boost/optional/optional.hpp:59, - from /usr/include/boost/optional.hpp:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref_reductions.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/flex_grid.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:15, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:3: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared_plain >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:769:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 769 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 770 | shared_plain, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ - 771 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 772 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:32:47: required from here - 32 | flex_wrapper >::plain("tiny_size_t_2") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:773:52: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ - 773 | scitbx::boost_python::container_conversions::from_python_sequence< - | ^~~~~~~~~~~~~~~~~~~~~ - 774 | shared, - | ~~~~~~~~~~~~~~~~~~~~ - 775 | scitbx::boost_python::container_conversions - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 776 | ::variable_capacity_policy>(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:32:47: required from here 32 | flex_wrapper >::plain("tiny_size_t_2") | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:18: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘scitbx::af::versa > scitbx::af::copy_slice(const const_ref >&, small) [with T = tiny]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:202:29: required from ‘static scitbx::af::versa > scitbx::af::boost_python::flex_wrapper::getitem_nd_slice(const scitbx::af::const_ref >&, const scitbx::af::small&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 202 | return copy_slice(self, slices_simple); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:228:54: required from ‘static boost::python::api::object scitbx::af::boost_python::flex_wrapper::getitem_tuple(boost::python::api::object&, boost::python::api::object) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy]’ - 228 | return boost::python::object(getitem_nd_slice(a.const_ref(), slices)); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:806:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 89 | for (int i=0;i >&, small, const const_ref >&) [with T = tiny]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ + 269 | copy_to_slice(self, slices_simple, other.const_ref()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy]’ + 289 | setitem_nd_slice(a, slices, b); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -25455,21 +25479,32 @@ 805 | .def("capacity", capacity) | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 806 | .def("__getitem__", getitem_tuple) // must be before other __getitem__ + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 807 | .def("__getitem__", getitem_1d_slice) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 808 | .def("__getitem__", getitem_1d, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 809 | .def("__getitem_fgdit__", getitem_fgdit, GetitemReturnValuePolicy()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:32:47: required from here 32 | flex_wrapper >::plain("tiny_size_t_2") | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 89 | for (int i=0;i >&, small, const const_ref >&) [with T = tiny]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h: In instantiation of ‘void scitbx::af::detail::copy_to_slice_detail(scitbx::af::versa >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = scitbx::mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = scitbx::mat3]’ + 119 | detail::copy_to_slice_detail(self, slices, other); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:269:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_nd_slice(f_t&, const scitbx::af::small&, const f_t&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; f_t = scitbx::af::versa, scitbx::af::flex_grid<> >]’ 269 | copy_to_slice(self, slices_simple, other.const_ref()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:289:25: required from ‘static void scitbx::af::boost_python::flex_wrapper::setitem_tuple(boost::python::api::object&, boost::python::api::object, boost::python::api::object&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy]’ 289 | setitem_nd_slice(a, slices, b); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::af::tiny; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:810:13: required from ‘static scitbx::af::boost_python::flex_wrapper::class_f_t scitbx::af::boost_python::flex_wrapper::plain(const std::string&) [with ElementType = scitbx::mat3; GetitemReturnValuePolicy = boost::python::return_value_policy; class_f_t = boost::python::class_, scitbx::af::flex_grid<> >, scitbx::af::boost_python::flex_wrapper >, boost::python::detail::not_specified, boost::python::detail::not_specified>; std::string = std::__cxx11::basic_string]’ 782 | result | ~~~~~~ 783 | .def(init const&, optional >()) @@ -25528,12 +25563,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 810 | .def("__setitem__", setitem_tuple) // must be before other __setitem__ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_tiny_size_t_2.cpp:32:47: required from here - 32 | flex_wrapper >::plain("tiny_size_t_2") - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:114:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 114 | for (int i=0;i >&, scitbx::af::small, const scitbx::af::const_ref >&) [with T = scitbx::af::tiny]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:119:35: required from ‘void scitbx::af::copy_to_slice(versa >&, small, const const_ref >&) [with T = tiny]’ 119 | detail::copy_to_slice_detail(self, slices, other); @@ -25608,10 +25642,40 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/slice.h:70:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if (idx_a[j] < slices[j].stop) break; +g++ -o scitbx/array_family/boost_python/numpy_bridge.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -DSCITBX_HAVE_NUMPY_INCLUDE -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/array_family/boost_python/shared_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/shared_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/cubicle_neighbors_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicle_neighbors_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::vec3; AccessorType = scitbx::af::flex_grid<>]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::vec3]’ declared here + 165 | void resize(size_type const& new_size, ElementType const& x) { + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ^~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::af::tiny; AccessorType = scitbx::af::flex_grid<>]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::af::tiny&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::af::tiny]’ declared here + 165 | void resize(size_type const& new_size, ElementType const& x) { + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ^~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp: In instantiation of ‘boost::python::api::object scitbx::af::boost_python::ref_flex_as_numpy_array(const scitbx::af::ref >&, bool, int) [with ElementType = bool]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp:202:3: required from here 191 | return ref_flex_as_numpy_array(O, optional, type_num); \ @@ -25724,6 +25788,29 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp:138:5: note: in expansion of macro ‘SCITBX_ASSERT’ 138 | SCITBX_ASSERT(grid.size_1d() == PyArray_Size(obj_ptr)); | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::af::tiny]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/memory:71, + from /usr/include/boost/function/function_base.hpp:33, + from /usr/include/boost/function/detail/prologue.hpp:18, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/to_python_value.hpp:14, + from /usr/include/boost/python/default_call_policies.hpp:10, + from /usr/include/boost/python/make_function.hpp:10, + from /usr/include/boost/python/def.hpp:11, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::af::tiny&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::af::tiny*; _Size = long unsigned int; _Tp = scitbx::af::tiny]’ declared here + 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ^~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp: In instantiation of ‘boost::python::api::object scitbx::af::boost_python::ref_flex_as_numpy_array(const scitbx::af::ref >&, bool, int) [with ElementType = double]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp:206:3: required from here 191 | return ref_flex_as_numpy_array(O, optional, type_num); \ @@ -25940,6 +26027,119 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/numpy_bridge.cpp:138:5: note: in expansion of macro ‘SCITBX_ASSERT’ 138 | SCITBX_ASSERT(grid.size_1d() == PyArray_Size(obj_ptr)); | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/memory:71, + from /usr/include/boost/function/function_base.hpp:33, + from /usr/include/boost/function/detail/prologue.hpp:18, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/to_python_value.hpp:14, + from /usr/include/boost/python/default_call_policies.hpp:10, + from /usr/include/boost/python/make_function.hpp:10, + from /usr/include/boost/python/def.hpp:11, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ declared here + 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ^~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::sym_mat3; AccessorType = scitbx::af::flex_grid<>]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::sym_mat3&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::sym_mat3]’ declared here + 165 | void resize(size_type const& new_size, ElementType const& x) { + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::sym_mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/memory:71, + from /usr/include/boost/function/function_base.hpp:33, + from /usr/include/boost/function/detail/prologue.hpp:18, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/to_python_value.hpp:14, + from /usr/include/boost/python/default_call_policies.hpp:10, + from /usr/include/boost/python/make_function.hpp:10, + from /usr/include/boost/python/def.hpp:11, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::sym_mat3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::sym_mat3*; _Size = long unsigned int; _Tp = scitbx::sym_mat3]’ declared here + 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ^~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::mat3; AccessorType = scitbx::af::flex_grid<>]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::mat3&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::mat3]’ declared here + 165 | void resize(size_type const& new_size, ElementType const& x) { + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ^~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/memory:71, + from /usr/include/boost/function/function_base.hpp:33, + from /usr/include/boost/function/detail/prologue.hpp:18, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/to_python_value.hpp:14, + from /usr/include/boost/python/default_call_policies.hpp:10, + from /usr/include/boost/python/make_function.hpp:10, + from /usr/include/boost/python/def.hpp:11, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::mat3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::mat3*; _Size = long unsigned int; _Tp = scitbx::mat3]’ declared here + 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ^~~~~~~~~~~~~ +g++ -o scitbx/fftpack/boost_python/fftpack_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/boost_python/fftpack_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::vec2; AccessorType = scitbx::af::flex_grid<>]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::vec2&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::vec2]’ declared here + 165 | void resize(size_type const& new_size, ElementType const& x) { + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here + 168 | base_class::resize(m_accessor.size_1d(), ElementType()); + | ^~~~~~~~~~~~~ In file included from /usr/include/c++/15/cassert:46, from /usr/include/boost/move/detail/type_traits.hpp:33, from /usr/include/boost/move/traits.hpp:31, @@ -25971,20 +26171,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::vec3; AccessorType = scitbx::af::flex_grid<>]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::vec3]’ declared here - 165 | void resize(size_type const& new_size, ElementType const& x) { - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ^~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::shared >; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ 146 | &convertible, @@ -26099,97 +26285,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/memory:71, - from /usr/include/boost/function/function_base.hpp:33, - from /usr/include/boost/function/detail/prologue.hpp:18, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/to_python_value.hpp:14, - from /usr/include/boost/python/default_call_policies.hpp:10, - from /usr/include/boost/python/make_function.hpp:10, - from /usr/include/boost/python/def.hpp:11, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ declared here - 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::sym_mat3; AccessorType = scitbx::af::flex_grid<>]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::sym_mat3&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::sym_mat3]’ declared here - 165 | void resize(size_type const& new_size, ElementType const& x) { - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::sym_mat3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/memory:71, - from /usr/include/boost/function/function_base.hpp:33, - from /usr/include/boost/function/detail/prologue.hpp:18, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/to_python_value.hpp:14, - from /usr/include/boost/python/default_call_policies.hpp:10, - from /usr/include/boost/python/make_function.hpp:10, - from /usr/include/boost/python/def.hpp:11, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::sym_mat3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::sym_mat3*; _Size = long unsigned int; _Tp = scitbx::sym_mat3]’ declared here - 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ^~~~~~~~~~~~~ -g++ -o scitbx/fftpack/boost_python/fftpack_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/boost_python/fftpack_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::vec2; AccessorType = scitbx::af::flex_grid<>]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::vec2&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::vec2]’ declared here - 165 | void resize(size_type const& new_size, ElementType const& x) { - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::af::tiny; AccessorType = scitbx::af::flex_grid<>]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::af::tiny&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::af::tiny]’ declared here - 165 | void resize(size_type const& new_size, ElementType const& x) { - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::af::tiny]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec2]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26206,7 +26302,7 @@ from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::af::tiny&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::af::tiny*; _Size = long unsigned int; _Tp = scitbx::af::tiny]’ declared here +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec2&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec2*; _Size = long unsigned int; _Tp = scitbx::vec2]’ declared here 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here @@ -26214,42 +26310,19 @@ | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::mat3; AccessorType = scitbx::af::flex_grid<>]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::vec3; AccessorType = scitbx::af::flex_grid<>]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 168 | base_class::resize(m_accessor.size_1d(), ElementType()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::mat3&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::mat3]’ declared here +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::vec3]’ declared here 165 | void resize(size_type const& new_size, ElementType const& x) { | ^~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here 168 | base_class::resize(m_accessor.size_1d(), ElementType()); | ^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec2]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/memory:71, - from /usr/include/boost/function/function_base.hpp:33, - from /usr/include/boost/function/detail/prologue.hpp:18, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/to_python_value.hpp:14, - from /usr/include/boost/python/default_call_policies.hpp:10, - from /usr/include/boost/python/make_function.hpp:10, - from /usr/include/boost/python/def.hpp:11, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec2&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec2*; _Size = long unsigned int; _Tp = scitbx::vec2]’ declared here - 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::mat3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -26266,26 +26339,12 @@ from /usr/include/boost/python/make_function.hpp:10, from /usr/include/boost/python/def.hpp:11, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::mat3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::mat3*; _Size = long unsigned int; _Tp = scitbx::mat3]’ declared here +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ declared here 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/flex_types.h:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘void scitbx::af::versa_plain::resize(const AccessorType&) [with ElementType = scitbx::vec3; AccessorType = scitbx::af::flex_grid<>]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:27: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:165:12: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘void scitbx::af::shared_plain::resize(const size_type&, const ElementType&) [with ElementType = scitbx::vec3]’ declared here - 165 | void resize(size_type const& new_size, ElementType const& x) { - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:168:50: note: ‘’ declared here - 168 | base_class::resize(m_accessor.size_1d(), ElementType()); - | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicle_neighbors_ext.cpp:3: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicle_neighbors.hpp: In instantiation of ‘std::map > scitbx::cubicle_neighbors::neighbors_of(const scitbx::af::const_ref >&, const FloatType&) [with FloatType = double]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicle_neighbors_ext.cpp:23:36: required from here @@ -26297,10 +26356,6 @@ 63 | if (i_cub[1] < 0 || i_cub[1] >= n_cubicles[1]) continue; /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicle_neighbors.hpp:65:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 65 | if (i_cub[2] < 0 || i_cub[2] >= n_cubicles[2]) continue; -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicle_neighbors.hpp:4: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicles.h: In instantiation of ‘scitbx::vec3 scitbx::cubicles::i_cubicle(const SiteType&) const [with SiteType = scitbx::vec3; CubicleContentType = std::vector::cubicle_site, std::allocator::cubicle_site> >; FloatType = double]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicle_neighbors.hpp:43:30: required from ‘scitbx::cubicle_neighbors::cubicle_neighbors(const scitbx::af::const_ref >&, const FloatType&, const FloatType&) [with FloatType = double]’ @@ -26387,27 +26442,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/cubicles.h:176:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 176 | else if (j >= ref.accessor()[i]) j = ref.accessor()[i]-1; | ~~^~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/memory:71, - from /usr/include/boost/function/function_base.hpp:33, - from /usr/include/boost/function/detail/prologue.hpp:18, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/to_python_value.hpp:14, - from /usr/include/boost/python/default_call_policies.hpp:10, - from /usr/include/boost/python/make_function.hpp:10, - from /usr/include/boost/python/def.hpp:11, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/flex_wrapper.h:6: -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ declared here - 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ^~~~~~~~~~~~~ -g++ -o scitbx/glmtbx/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/glmtbx/boost_python/ext.cc -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/gridding.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/boost_python/fftpack_ext.cpp:4: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/factorization.h: In constructor ‘scitbx::fftpack::factorization::factorization(std::size_t, bool)’: @@ -26417,6 +26451,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/factorization.h:67:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::tiny_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 67 | for (i = 0; i < opt_factors.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/glmtbx/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/glmtbx/boost_python/ext.cc +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/graphics_utils/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/graphics_utils/ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/scitbx_cubicle_neighbors_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_cubicle_neighbors_ext.so.0 scitbx/cubicle_neighbors_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -26429,8 +26467,6 @@ Create symlinks for: 'lib/scitbx_cubicle_neighbors_ext.so.0.0.1' 'lib/scitbx_cubicle_neighbors_ext.so.0'->'lib/scitbx_cubicle_neighbors_ext.so.0.0.1' 'lib/scitbx_cubicle_neighbors_ext.so'->'lib/scitbx_cubicle_neighbors_ext.so.0.0.1' -g++ -o scitbx/graphics_utils/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/graphics_utils/ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/iso_surface/iso_surface_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/iso_surface/iso_surface_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/lbfgs/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DSCITBX_LBFGS_HAVE_LBFGS_FEM -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgs/ext.cpp @@ -26476,6 +26512,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/write.hpp:704:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 704 | while (pos < internal_file_len) { | ~~~~^~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/linalg/boost_python/linalg_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/linalg_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/serialization/base_256.h:2, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/floating_point_epsilon.h:4, @@ -26738,6 +26776,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/raw.h:188:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 188 | for(int j=0;j::minimizer(const int&, const int&, scitbx::af::shared, scitbx::af::shared, scitbx::af::shared, bool, const FloatType&, const FloatType&, const int&) [with FloatType = double]’: /usr/include/boost/python/object/value_holder.hpp:131:11: required from ‘boost::python::objects::value_holder::value_holder(PyObject*, A0, A1, A2, A3, A4, A5, A6, A7, A8) [with A0 = boost::python::objects::reference_to_value; A1 = boost::python::objects::reference_to_value; A2 = boost::python::objects::reference_to_value >; A3 = boost::python::objects::reference_to_value >; A4 = boost::python::objects::reference_to_value >; A5 = bool; A6 = boost::python::objects::reference_to_value; A7 = boost::python::objects::reference_to_value; A8 = boost::python::objects::reference_to_value; Value = scitbx::lbfgsb::minimizer; PyObject = _object]’ 131 | PyObject* self BOOST_PP_COMMA_IF(N) BOOST_PP_ENUM_BINARY_PARAMS_Z(1, N, A, a)) @@ -26848,15 +26890,9 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb.h:120:9: note: in expansion of macro ‘SCITBX_ASSERT’ 120 | SCITBX_ASSERT(nbd.size() == n); | ^~~~~~~~~~~~~ -g++ -o scitbx/linalg/boost_python/linalg_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/linalg_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/linalg/boost_python/matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/matrix.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/linalg/boost_python/cholesky.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/cholesky.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/linalg/boost_python/householder.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/householder.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_glmtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_glmtbx_ext.so.0 scitbx/glmtbx/boost_python/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/scitbx_iso_surface_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_iso_surface_ext.so.0 scitbx/iso_surface/iso_surface_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -26865,12 +26901,12 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_glmtbx_ext.so.0.0.1' - 'lib/scitbx_glmtbx_ext.so.0'->'lib/scitbx_glmtbx_ext.so.0.0.1' - 'lib/scitbx_glmtbx_ext.so'->'lib/scitbx_glmtbx_ext.so.0.0.1' +Create symlinks for: 'lib/scitbx_iso_surface_ext.so.0.0.1' + 'lib/scitbx_iso_surface_ext.so.0'->'lib/scitbx_iso_surface_ext.so.0.0.1' + 'lib/scitbx_iso_surface_ext.so'->'lib/scitbx_iso_surface_ext.so.0.0.1' g++ -o scitbx/linalg/boost_python/svd.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/svd.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_iso_surface_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_iso_surface_ext.so.0 scitbx/iso_surface/iso_surface_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/scitbx_glmtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_glmtbx_ext.so.0 scitbx/glmtbx/boost_python/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -26879,9 +26915,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_iso_surface_ext.so.0.0.1' - 'lib/scitbx_iso_surface_ext.so.0'->'lib/scitbx_iso_surface_ext.so.0.0.1' - 'lib/scitbx_iso_surface_ext.so'->'lib/scitbx_iso_surface_ext.so.0.0.1' +Create symlinks for: 'lib/scitbx_glmtbx_ext.so.0.0.1' + 'lib/scitbx_glmtbx_ext.so.0'->'lib/scitbx_glmtbx_ext.so.0.0.1' + 'lib/scitbx_glmtbx_ext.so'->'lib/scitbx_glmtbx_ext.so.0.0.1' g++ -o scitbx/linalg/boost_python/eigensystem.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/eigensystem.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/scitbx_graphics_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_graphics_utils_ext.so.0 scitbx/graphics_utils/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm @@ -26900,75 +26936,76 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/lstbx/boost_python/lstbx_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lstbx/boost_python/lstbx_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sym_mat3.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp:5: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp: In function ‘int scitbx::lapack::boost_python::dsyev_wrapper(const std::string&, const std::string&, const scitbx::af::ref >&, const scitbx::af::ref&, bool)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp:246:28: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 246 | SCITBX_ASSERT(w.size() == n); - | ~~~~~~~~~^~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ - 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ - | ^~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp:246:5: note: in expansion of macro ‘SCITBX_ASSERT’ - 246 | SCITBX_ASSERT(w.size() == n); - | ^~~~~~~~~~~~~ g++ -o scitbx/lstbx/boost_python/normal_equations.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lstbx/boost_python/normal_equations.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_lbfgsb_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_lbfgsb_ext.so.0 scitbx/lbfgsb/boost_python/lbfgsb_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -lboost_timer +g++ -o lib/scitbx_fftpack_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_fftpack_ext.so.0 scitbx/fftpack/boost_python/fftpack_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_timer.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_lbfgsb_ext.so.0.0.1' - 'lib/scitbx_lbfgsb_ext.so.0'->'lib/scitbx_lbfgsb_ext.so.0.0.1' - 'lib/scitbx_lbfgsb_ext.so'->'lib/scitbx_lbfgsb_ext.so.0.0.1' +Create symlinks for: 'lib/scitbx_fftpack_ext.so.0.0.1' + 'lib/scitbx_fftpack_ext.so.0'->'lib/scitbx_fftpack_ext.so.0.0.1' + 'lib/scitbx_fftpack_ext.so'->'lib/scitbx_fftpack_ext.so.0.0.1' g++ -o scitbx/math/boost_python/math_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/math_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_fftpack_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_fftpack_ext.so.0 scitbx/fftpack/boost_python/fftpack_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/scitbx_lbfgsb_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_lbfgsb_ext.so.0 scitbx/lbfgsb/boost_python/lbfgsb_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -lboost_timer /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_timer.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_fftpack_ext.so.0.0.1' - 'lib/scitbx_fftpack_ext.so.0'->'lib/scitbx_fftpack_ext.so.0.0.1' - 'lib/scitbx_fftpack_ext.so'->'lib/scitbx_fftpack_ext.so.0.0.1' +Create symlinks for: 'lib/scitbx_lbfgsb_ext.so.0.0.1' + 'lib/scitbx_lbfgsb_ext.so.0'->'lib/scitbx_lbfgsb_ext.so.0.0.1' + 'lib/scitbx_lbfgsb_ext.so'->'lib/scitbx_lbfgsb_ext.so.0.0.1' g++ -o scitbx/math/boost_python/basic_statistics.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/basic_statistics.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sym_mat3.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp:5: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp: In function ‘int scitbx::lapack::boost_python::dsyev_wrapper(const std::string&, const std::string&, const scitbx::af::ref >&, const scitbx::af::ref&, bool)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp:246:28: warning: comparison of integer expressions of different signedness: ‘scitbx::af::const_ref::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 246 | SCITBX_ASSERT(w.size() == n); + | ~~~~~~~~~^~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error_utils.h:166:9: note: in definition of macro ‘SCITBX_ERROR_UTILS_ASSERT’ + 166 | if (!(assertion)) throw error_class(__FILE__, __LINE__, \ + | ^~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/linalg/boost_python/lapack_fem_bpl.cpp:246:5: note: in expansion of macro ‘SCITBX_ASSERT’ + 246 | SCITBX_ASSERT(w.size() == n); + | ^~~~~~~~~~~~~ g++ -o scitbx/math/boost_python/gaussian.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/gaussian.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/math/boost_python/golay.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/golay.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/math/boost_python/minimum_covering_sphere.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/minimum_covering_sphere.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/math/boost_python/principal_axes_of_inertia.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/principal_axes_of_inertia.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_array_family_shared_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_array_family_shared_ext.so.0 scitbx/array_family/boost_python/shared_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -lboost_numpy313 +g++ -o lib/scitbx_lbfgs_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_lbfgs_ext.so.0 scitbx/lbfgs/ext.o scitbx/lbfgs/lbfgs_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_numpy313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_array_family_shared_ext.so.0.0.1' - 'lib/scitbx_array_family_shared_ext.so.0'->'lib/scitbx_array_family_shared_ext.so.0.0.1' - 'lib/scitbx_array_family_shared_ext.so'->'lib/scitbx_array_family_shared_ext.so.0.0.1' +g++ -o scitbx/math/boost_python/principal_axes_of_inertia.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/principal_axes_of_inertia.cpp +Create symlinks for: 'lib/scitbx_lbfgs_ext.so.0.0.1' + 'lib/scitbx_lbfgs_ext.so.0'->'lib/scitbx_lbfgs_ext.so.0.0.1' + 'lib/scitbx_lbfgs_ext.so'->'lib/scitbx_lbfgs_ext.so.0.0.1' +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/math/boost_python/row_echelon.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/row_echelon.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_lbfgs_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_lbfgs_ext.so.0 scitbx/lbfgs/ext.o scitbx/lbfgs/lbfgs_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o scitbx/math/boost_python/tensor_rank_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/tensor_rank_2.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/scitbx_linalg_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_linalg_ext.so.0 scitbx/linalg/boost_python/linalg_ext.o scitbx/linalg/boost_python/matrix.o scitbx/linalg/boost_python/cholesky.o scitbx/linalg/boost_python/householder.o scitbx/linalg/boost_python/svd.o scitbx/linalg/boost_python/eigensystem.o scitbx/linalg/boost_python/lapack_fem_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -26977,29 +27014,28 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/scitbx_linalg_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_linalg_ext.so.0 scitbx/linalg/boost_python/linalg_ext.o scitbx/linalg/boost_python/matrix.o scitbx/linalg/boost_python/cholesky.o scitbx/linalg/boost_python/householder.o scitbx/linalg/boost_python/svd.o scitbx/linalg/boost_python/eigensystem.o scitbx/linalg/boost_python/lapack_fem_bpl.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o scitbx/math/boost_python/tensor_rank_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/tensor_rank_2.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/scitbx_lbfgs_ext.so.0.0.1' - 'lib/scitbx_lbfgs_ext.so.0'->'lib/scitbx_lbfgs_ext.so.0.0.1' - 'lib/scitbx_lbfgs_ext.so'->'lib/scitbx_lbfgs_ext.so.0.0.1' +Create symlinks for: 'lib/scitbx_linalg_ext.so.0.0.1' + 'lib/scitbx_linalg_ext.so.0'->'lib/scitbx_linalg_ext.so.0.0.1' + 'lib/scitbx_linalg_ext.so'->'lib/scitbx_linalg_ext.so.0.0.1' g++ -o scitbx/math/boost_python/chebyshev.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/chebyshev.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/math/boost_python/icosahedron.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/icosahedron.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/scitbx_array_family_shared_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_array_family_shared_ext.so.0 scitbx/array_family/boost_python/shared_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -lboost_numpy313 /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_numpy313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o scitbx/math/boost_python/icosahedron.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/icosahedron.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/scitbx_linalg_ext.so.0.0.1' - 'lib/scitbx_linalg_ext.so.0'->'lib/scitbx_linalg_ext.so.0.0.1' - 'lib/scitbx_linalg_ext.so'->'lib/scitbx_linalg_ext.so.0.0.1' g++ -o scitbx/math/boost_python/slatec.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/slatec.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/scitbx_array_family_shared_ext.so.0.0.1' + 'lib/scitbx_array_family_shared_ext.so.0'->'lib/scitbx_array_family_shared_ext.so.0.0.1' + 'lib/scitbx_array_family_shared_ext.so'->'lib/scitbx_array_family_shared_ext.so.0.0.1' g++ -o scitbx/math/boost_python/line_search.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/line_search.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/math/boost_python/r3_rotation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/r3_rotation.cpp @@ -27010,11 +27046,9 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/math/boost_python/unimodular_generator.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/unimodular_generator.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/scitbx_lstbx_normal_equations_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_lstbx_normal_equations_ext.so.0 scitbx/lstbx/boost_python/lstbx_ext.o scitbx/lstbx/boost_python/normal_equations.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm g++ -o scitbx/math/boost_python/halton.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/halton.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/math/boost_python/least_squares_plane.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/least_squares_plane.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_lstbx_normal_equations_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_lstbx_normal_equations_ext.so.0 scitbx/lstbx/boost_python/lstbx_ext.o scitbx/lstbx/boost_python/normal_equations.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27026,6 +27060,8 @@ Create symlinks for: 'lib/scitbx_lstbx_normal_equations_ext.so.0.0.1' 'lib/scitbx_lstbx_normal_equations_ext.so.0'->'lib/scitbx_lstbx_normal_equations_ext.so.0.0.1' 'lib/scitbx_lstbx_normal_equations_ext.so'->'lib/scitbx_lstbx_normal_equations_ext.so.0.0.1' +g++ -o scitbx/math/boost_python/least_squares_plane.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/least_squares_plane.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/math/boost_python/continued_fraction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/continued_fraction.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/math/boost_python/numeric_limits.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/boost_python/numeric_limits.cpp @@ -27054,8 +27090,6 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/r3_utils_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/r3_utils_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/random/boost_python/random_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/random/boost_python/random_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/minpack/raw.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/minpack/levenberg_marquardt.h:4, @@ -27070,6 +27104,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/minpack/levenberg_marquardt.h:80:9: note: in expansion of macro ‘SCITBX_ASSERT’ 80 | SCITBX_ASSERT(fvec.size() == m); | ^~~~~~~~~~~~~ +g++ -o scitbx/random/boost_python/random_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/random/boost_python/random_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/random/boost_python/basic_distributions.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/random/boost_python/basic_distributions.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/rigid_body/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/rigid_body/ext.cpp @@ -27077,7 +27113,6 @@ g++ -o scitbx/sparse/boost_python/vector.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/vector.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/scitbx_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_array_family_flex_ext.so.0 scitbx/array_family/boost_python/flex_ext.o scitbx/array_family/boost_python/flex_grid.o scitbx/array_family/boost_python/flex_bool.o scitbx/array_family/boost_python/flex_size_t.o scitbx/array_family/boost_python/flex_int.o scitbx/array_family/boost_python/flex_float.o scitbx/array_family/boost_python/flex_double.o scitbx/array_family/boost_python/flex_double_matrix.o scitbx/array_family/boost_python/flex_complex_double.o scitbx/array_family/boost_python/flex_std_string.o scitbx/array_family/boost_python/flex_random.o scitbx/array_family/boost_python/flex_sort.o scitbx/array_family/boost_python/flex_histogram.o scitbx/array_family/boost_python/flex_weighted_histogram.o scitbx/array_family/boost_python/flex_mean_and_variance.o scitbx/array_family/boost_python/flex_median.o scitbx/array_family/boost_python/flex_linear_interpolation.o scitbx/array_family/boost_python/flex_vec3_double.o scitbx/array_family/boost_python/flex_vec2_double.o scitbx/array_family/boost_python/flex_vec3_int.o scitbx/array_family/boost_python/flex_sym_mat3_double.o scitbx/array_family/boost_python/flex_mat3_double.o scitbx/array_family/boost_python/flex_tiny_size_t_2.o scitbx/array_family/boost_python/loops.o scitbx/array_family/boost_python/show_sizes.o scitbx/array_family/boost_python/numpy_bridge.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -lboost_numpy313 -g++ -o lib/scitbx_r3_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_r3_utils_ext.so.0 scitbx/r3_utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27087,7 +27122,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o scitbx/sparse/boost_python/matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/matrix.cpp +g++ -o lib/scitbx_r3_utils_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_r3_utils_ext.so.0 scitbx/r3_utils_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27096,11 +27131,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/scitbx_r3_utils_ext.so.0.0.1' 'lib/scitbx_r3_utils_ext.so.0'->'lib/scitbx_r3_utils_ext.so.0.0.1' 'lib/scitbx_r3_utils_ext.so'->'lib/scitbx_r3_utils_ext.so.0.0.1' -g++ -o scitbx/sparse/boost_python/approx_equal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/approx_equal.cpp +g++ -o scitbx/sparse/boost_python/matrix.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/matrix.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:6, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -27144,6 +27178,20 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:59:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 59 | if (N < last - first) throw_range_error(); | ~~^~~~~~~~~~~~~~ +g++ -o lib/scitbx_minpack_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_minpack_ext.so.0 scitbx/minpack/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_minpack -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/scitbx_minpack_ext.so.0.0.1' + 'lib/scitbx_minpack_ext.so.0'->'lib/scitbx_minpack_ext.so.0.0.1' + 'lib/scitbx_minpack_ext.so'->'lib/scitbx_minpack_ext.so.0.0.1' +g++ -o scitbx/sparse/boost_python/approx_equal.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/approx_equal.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error.h:16, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/mat3.h:5: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/rigid_body/tardy.h: In instantiation of ‘scitbx::af::shared > > scitbx::rigid_body::tardy::construct_bodies(const scitbx::af::const_ref >&, const scitbx::af::const_ref&, const boost::python::api::object&, const FloatType&) [with FloatType = double]’: @@ -27264,6 +27312,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/rigid_body/tardy.h:163:9: note: in expansion of macro ‘SCITBX_ASSERT’ 163 | SCITBX_ASSERT(body->parent < nc); | ^~~~~~~~~~~~~ +g++ -o scitbx/sparse/boost_python/random.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/random.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h: In instantiation of ‘scitbx::af::tiny::tiny(const OtherElementType*, const OtherElementType*) [with OtherElementType = double; ElementType = double; long unsigned int N = 1]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/rigid_body/joint_lib.h:648:13: required from ‘boost::shared_ptr > scitbx::rigid_body::joint_lib::revolute::new_q(const scitbx::af::const_ref&) const [with FloatType = double]’ 648 | af::tiny(q.begin(), q.end()))); @@ -27277,7 +27327,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:30:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_TINY_CONVENIENCE_CONSTRUCTORS’ 30 | SCITBX_ARRAY_FAMILY_TINY_CONVENIENCE_CONSTRUCTORS(tiny) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o lib/scitbx_minpack_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_minpack_ext.so.0 scitbx/minpack/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_minpack -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h: In instantiation of ‘scitbx::af::tiny::tiny(const OtherElementType*, const OtherElementType*) [with OtherElementType = double; ElementType = double; long unsigned int N = 12]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/rigid_body/joint_lib.h:45:16: required from ‘scitbx::af::tiny scitbx::rigid_body::joint_lib::rbda_eq_4_13(const scitbx::af::tiny&) [with FloatType = double]’ 45 | return af::tiny(coeffs, coeffs+4*3) * ft(0.5); @@ -27323,28 +27372,15 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:59:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 59 | if (N < last - first) throw_range_error(); | ~~^~~~~~~~~~~~~~ -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_minpack_ext.so.0.0.1' - 'lib/scitbx_minpack_ext.so.0'->'lib/scitbx_minpack_ext.so.0.0.1' - 'lib/scitbx_minpack_ext.so'->'lib/scitbx_minpack_ext.so.0.0.1' -g++ -o scitbx/sparse/boost_python/random.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/random.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/sparse/boost_python/lu_factorization.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/lu_factorization.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/scitbx_array_family_flex_ext.so.0.0.1' + 'lib/scitbx_array_family_flex_ext.so.0'->'lib/scitbx_array_family_flex_ext.so.0.0.1' + 'lib/scitbx_array_family_flex_ext.so'->'lib/scitbx_array_family_flex_ext.so.0.0.1' g++ -o scitbx/sparse/boost_python/sparse_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/boost_python/sparse_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/stl/map_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/stl/map_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/scitbx_array_family_flex_ext.so.0.0.1' - 'lib/scitbx_array_family_flex_ext.so.0'->'lib/scitbx_array_family_flex_ext.so.0.0.1' - 'lib/scitbx_array_family_flex_ext.so'->'lib/scitbx_array_family_flex_ext.so.0.0.1' g++ -o scitbx/stl/set_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/stl/set_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/stl/vector_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/stl/vector_ext.cpp @@ -27370,8 +27406,6 @@ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ -g++ -o scitbx/suffixtree/boost_python/suffixtree_single_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/suffixtree/boost_python/suffixtree_single_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_ptr.hpp:25, from /usr/include/boost/shared_ptr.hpp:17, @@ -27407,40 +27441,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_matrix.h:4: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/memory:71, - from /usr/include/boost/config/no_tr1/memory.hpp:21, - from /usr/include/boost/get_pointer.hpp:14, - from /usr/include/boost/python/object/pointer_holder.hpp:11, - from /usr/include/boost/python/to_python_indirect.hpp:10, - from /usr/include/boost/python/converter/arg_to_python.hpp:10, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object.hpp:9, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/array_as_list.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/rigid_body/ext.cpp:3: -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ declared here - 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ^~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::af::tiny]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::af::tiny&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::af::tiny*; _Size = long unsigned int; _Tp = scitbx::af::tiny]’ declared here - 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here - 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); - | ^~~~~~~~~~~~~ In file included from /usr/include/boost/assert.hpp:58, from /usr/include/boost/smart_ptr/shared_ptr.hpp:25, from /usr/include/boost/shared_ptr.hpp:17, @@ -27509,8 +27509,58 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 197 | if (!is_range) assert(i == obj_size); | ~~^~~~~~~~~~~ +g++ -o scitbx/suffixtree/boost_python/suffixtree_single_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/suffixtree/boost_python/suffixtree_single_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:5, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_matrix.h:4: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::vec3]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/memory:71, + from /usr/include/boost/config/no_tr1/memory.hpp:21, + from /usr/include/boost/get_pointer.hpp:14, + from /usr/include/boost/python/object/pointer_holder.hpp:11, + from /usr/include/boost/python/to_python_indirect.hpp:10, + from /usr/include/boost/python/converter/arg_to_python.hpp:10, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/object.hpp:9, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/array_as_list.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/rigid_body/ext.cpp:3: +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::vec3&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::vec3*; _Size = long unsigned int; _Tp = scitbx::vec3]’ declared here + 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ^~~~~~~~~~~~~ +g++ -o lib/scitbx_suffixtree_shared_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_suffixtree_shared_ext.so.0 scitbx/suffixtree/boost_python/suffixtree_shared_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/scitbx_suffixtree_shared_ext.so.0.0.1' + 'lib/scitbx_suffixtree_shared_ext.so.0'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' + 'lib/scitbx_suffixtree_shared_ext.so'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' g++ -o scitbx/suffixtree/boost_python/object_extensions.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/suffixtree/boost_python/object_extensions.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In constructor ‘scitbx::af::shared_plain::shared_plain(const size_type&) [with ElementType = scitbx::af::tiny]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:34: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_uninitialized.h:526:5: note: by argument 3 of type ‘const scitbx::af::tiny&’ to ‘_ForwardIterator std::uninitialized_fill_n(_ForwardIterator, _Size, const _Tp&) [with _ForwardIterator = scitbx::af::tiny*; _Size = long unsigned int; _Tp = scitbx::af::tiny]’ declared here + 526 | uninitialized_fill_n(_ForwardIterator __first, _Size __n, const _Tp& __x) + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:132:48: note: ‘’ declared here + 132 | std::uninitialized_fill_n(begin(), sz, ElementType()); + | ^~~~~~~~~~~~~ +g++ -o scitbx/wigner/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/wigner/ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:307: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h: In member function ‘void scitbx::af::shared_plain::resize(const size_type&) [with ElementType = scitbx::af::tiny]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/push_back_etc.h:175:15: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] @@ -27534,24 +27584,12 @@ Create symlinks for: 'lib/scitbx_random_ext.so.0.0.1' 'lib/scitbx_random_ext.so.0'->'lib/scitbx_random_ext.so.0.0.1' 'lib/scitbx_random_ext.so'->'lib/scitbx_random_ext.so.0.0.1' -g++ -o lib/scitbx_suffixtree_shared_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_suffixtree_shared_ext.so.0 scitbx/suffixtree/boost_python/suffixtree_shared_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o scitbx/wigner/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/wigner/ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_suffixtree_shared_ext.so.0.0.1' - 'lib/scitbx_suffixtree_shared_ext.so.0'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' - 'lib/scitbx_suffixtree_shared_ext.so'->'lib/scitbx_suffixtree_shared_ext.so.0.0.1' g++ -o smtbx/ab_initio/ab_initio_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/ab_initio/ab_initio_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/array_family/af_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/array_family/af_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o smtbx/refinement/constraints/boost_python/affine.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/affine.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/scitbx_stl_set_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_stl_set_ext.so.0 scitbx/stl/set_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27564,13 +27602,11 @@ Create symlinks for: 'lib/scitbx_stl_set_ext.so.0.0.1' 'lib/scitbx_stl_set_ext.so.0'->'lib/scitbx_stl_set_ext.so.0.0.1' 'lib/scitbx_stl_set_ext.so'->'lib/scitbx_stl_set_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/affine.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/affine.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/refinement/constraints/boost_python/constraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/constraints_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_math_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_math_ext.so.0 scitbx/math/boost_python/math_ext.o scitbx/math/boost_python/basic_statistics.o scitbx/math/boost_python/gaussian.o scitbx/math/boost_python/golay.o scitbx/math/boost_python/minimum_covering_sphere.o scitbx/math/boost_python/principal_axes_of_inertia.o scitbx/math/boost_python/row_echelon.o scitbx/math/boost_python/tensor_rank_2.o scitbx/math/boost_python/chebyshev.o scitbx/math/boost_python/icosahedron.o scitbx/math/boost_python/slatec.o scitbx/math/boost_python/line_search.o scitbx/math/boost_python/r3_rotation.o scitbx/math/boost_python/resample.o scitbx/math/boost_python/quadrature.o scitbx/math/boost_python/unimodular_generator.o scitbx/math/boost_python/halton.o scitbx/math/boost_python/least_squares_plane.o scitbx/math/boost_python/continued_fraction.o scitbx/math/boost_python/numeric_limits.o scitbx/math/boost_python/distributions.o scitbx/math/boost_python/exp_functions.o scitbx/math/boost_python/zernike.o scitbx/math/boost_python/zernike_moments.o scitbx/math/boost_python/2d_zernike_moments.o scitbx/math/boost_python/weighted_covariance.o scitbx/math/boost_python/rotation.o scitbx/math/boost_python/interpolation.o scitbx/math/boost_python/tetrahedron.o scitbx/math/boost_python/angle_derivative.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_slatec -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm g++ -o smtbx/refinement/constraints/boost_python/direction.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/direction.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/scitbx_math_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_math_ext.so.0 scitbx/math/boost_python/math_ext.o scitbx/math/boost_python/basic_statistics.o scitbx/math/boost_python/gaussian.o scitbx/math/boost_python/golay.o scitbx/math/boost_python/minimum_covering_sphere.o scitbx/math/boost_python/principal_axes_of_inertia.o scitbx/math/boost_python/row_echelon.o scitbx/math/boost_python/tensor_rank_2.o scitbx/math/boost_python/chebyshev.o scitbx/math/boost_python/icosahedron.o scitbx/math/boost_python/slatec.o scitbx/math/boost_python/line_search.o scitbx/math/boost_python/r3_rotation.o scitbx/math/boost_python/resample.o scitbx/math/boost_python/quadrature.o scitbx/math/boost_python/unimodular_generator.o scitbx/math/boost_python/halton.o scitbx/math/boost_python/least_squares_plane.o scitbx/math/boost_python/continued_fraction.o scitbx/math/boost_python/numeric_limits.o scitbx/math/boost_python/distributions.o scitbx/math/boost_python/exp_functions.o scitbx/math/boost_python/zernike.o scitbx/math/boost_python/zernike_moments.o scitbx/math/boost_python/2d_zernike_moments.o scitbx/math/boost_python/weighted_covariance.o scitbx/math/boost_python/rotation.o scitbx/math/boost_python/interpolation.o scitbx/math/boost_python/tetrahedron.o scitbx/math/boost_python/angle_derivative.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_slatec -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27580,7 +27616,6 @@ /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. g++ -o lib/smtbx_ab_initio_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_ab_initio_ext.so.0 smtbx/ab_initio/ab_initio_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o lib/scitbx_sparse_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_sparse_ext.so.0 scitbx/sparse/boost_python/vector.o scitbx/sparse/boost_python/matrix.o scitbx/sparse/boost_python/approx_equal.o scitbx/sparse/boost_python/random.o scitbx/sparse/boost_python/lu_factorization.o scitbx/sparse/boost_python/sparse_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm g++ -o lib/smtbx_array_family_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_array_family_ext.so.0 smtbx/array_family/af_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27590,10 +27625,27 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.soCreate symlinks for: 'lib/smtbx_ab_initio_ext.so.0.0.1' +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/smtbx_ab_initio_ext.so.0.0.1' 'lib/smtbx_ab_initio_ext.so.0'->'lib/smtbx_ab_initio_ext.so.0.0.1' 'lib/smtbx_ab_initio_ext.so'->'lib/smtbx_ab_initio_ext.so.0.0.1' -: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o smtbx/refinement/constraints/boost_python/geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/geometrical_hydrogens.cpp +Create symlinks for: 'lib/smtbx_array_family_ext.so.0.0.1' + 'lib/smtbx_array_family_ext.so.0'->'lib/smtbx_array_family_ext.so.0.0.1' + 'lib/smtbx_array_family_ext.so'->'lib/smtbx_array_family_ext.so.0.0.1' +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o smtbx/refinement/constraints/boost_python/independent_scalar_parameters.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/independent_scalar_parameters.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/scitbx_sparse_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_sparse_ext.so.0 scitbx/sparse/boost_python/vector.o scitbx/sparse/boost_python/matrix.o scitbx/sparse/boost_python/approx_equal.o scitbx/sparse/boost_python/random.o scitbx/sparse/boost_python/lu_factorization.o scitbx/sparse/boost_python/sparse_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/scitbx_wigner_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_wigner_ext.so.0 scitbx/wigner/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27601,8 +27653,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_thread.sog++ -o smtbx/refinement/constraints/boost_python/geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/geometrical_hydrogens.cpp -: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27610,25 +27661,24 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/smtbx_array_family_ext.so.0.0.1' - 'lib/smtbx_array_family_ext.so.0'->'lib/smtbx_array_family_ext.so.0.0.1' - 'lib/smtbx_array_family_ext.so'->'lib/smtbx_array_family_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/independent_scalar_parameters.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/independent_scalar_parameters.cpp +Create symlinks for: 'lib/scitbx_wigner_ext.so.0.0.1' + 'lib/scitbx_wigner_ext.so.0'->'lib/scitbx_wigner_ext.so.0.0.1' + 'lib/scitbx_wigner_ext.so'->'lib/scitbx_wigner_ext.so.0.0.1' +g++ -o smtbx/refinement/constraints/boost_python/occupancy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/occupancy.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/scitbx_sparse_ext.so.0.0.1' 'lib/scitbx_sparse_ext.so.0'->'lib/scitbx_sparse_ext.so.0.0.1' 'lib/scitbx_sparse_ext.so'->'lib/scitbx_sparse_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/occupancy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/occupancy.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/refinement/constraints/boost_python/reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/reparametrisation.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o smtbx/refinement/constraints/boost_python/rigid.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/rigid.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ Create symlinks for: 'lib/scitbx_math_ext.so.0.0.1' 'lib/scitbx_math_ext.so.0'->'lib/scitbx_math_ext.so.0.0.1' 'lib/scitbx_math_ext.so'->'lib/scitbx_math_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/rigid.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/rigid.cpp +g++ -o smtbx/refinement/constraints/boost_python/same_group.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/same_group.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_wigner_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_wigner_ext.so.0 scitbx/wigner/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/scitbx_stl_vector_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_stl_vector_ext.so.0 scitbx/stl/vector_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27637,10 +27687,10 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_wigner_ext.so.0.0.1' - 'lib/scitbx_wigner_ext.so.0'->'lib/scitbx_wigner_ext.so.0.0.1' - 'lib/scitbx_wigner_ext.so'->'lib/scitbx_wigner_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/same_group.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/same_group.cpp +Create symlinks for: 'lib/scitbx_stl_vector_ext.so.0.0.1' + 'lib/scitbx_stl_vector_ext.so.0'->'lib/scitbx_stl_vector_ext.so.0.0.1' + 'lib/scitbx_stl_vector_ext.so'->'lib/scitbx_stl_vector_ext.so.0.0.1' +g++ -o smtbx/refinement/constraints/boost_python/scaled_adp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/scaled_adp.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/scitbx_rigid_body_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_rigid_body_ext.so.0 scitbx/rigid_body/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27654,29 +27704,17 @@ Create symlinks for: 'lib/scitbx_rigid_body_ext.so.0.0.1' 'lib/scitbx_rigid_body_ext.so.0'->'lib/scitbx_rigid_body_ext.so.0.0.1' 'lib/scitbx_rigid_body_ext.so'->'lib/scitbx_rigid_body_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/scaled_adp.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/scaled_adp.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/refinement/constraints/boost_python/scatterer_parameters.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/scatterer_parameters.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_stl_vector_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_stl_vector_ext.so.0 scitbx/stl/vector_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_stl_vector_ext.so.0.0.1' - 'lib/scitbx_stl_vector_ext.so.0'->'lib/scitbx_stl_vector_ext.so.0.0.1' - 'lib/scitbx_stl_vector_ext.so'->'lib/scitbx_stl_vector_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/boost_python/shared.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/shared.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/refinement/constraints/boost_python/special_position.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/special_position.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/refinement/constraints/boost_python/symmetry_equivalent.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/symmetry_equivalent.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_stl_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_stl_map_ext.so.0 scitbx/stl/map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/scitbx_suffixtree_single_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_suffixtree_single_ext.so.0 scitbx/suffixtree/boost_python/suffixtree_single_ext.o scitbx/suffixtree/boost_python/object_extensions.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27685,12 +27723,12 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_stl_map_ext.so.0.0.1' - 'lib/scitbx_stl_map_ext.so.0'->'lib/scitbx_stl_map_ext.so.0.0.1' - 'lib/scitbx_stl_map_ext.so'->'lib/scitbx_stl_map_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.cpp +Create symlinks for: 'lib/scitbx_suffixtree_single_ext.so.0.0.1' + 'lib/scitbx_suffixtree_single_ext.so.0'->'lib/scitbx_suffixtree_single_ext.so.0.0.1' + 'lib/scitbx_suffixtree_single_ext.so'->'lib/scitbx_suffixtree_single_ext.so.0.0.1' +g++ -o smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/scitbx_suffixtree_single_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_suffixtree_single_ext.so.0 scitbx/suffixtree/boost_python/suffixtree_single_ext.o scitbx/suffixtree/boost_python/object_extensions.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o lib/scitbx_stl_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=scitbx_stl_map_ext.so.0 scitbx/stl/map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27699,11 +27737,9 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/scitbx_suffixtree_single_ext.so.0.0.1' - 'lib/scitbx_suffixtree_single_ext.so.0'->'lib/scitbx_suffixtree_single_ext.so.0.0.1' - 'lib/scitbx_suffixtree_single_ext.so'->'lib/scitbx_suffixtree_single_ext.so.0.0.1' -g++ -o smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +Create symlinks for: 'lib/scitbx_stl_map_ext.so.0.0.1' + 'lib/scitbx_stl_map_ext.so.0'->'lib/scitbx_stl_map_ext.so.0.0.1' + 'lib/scitbx_stl_map_ext.so'->'lib/scitbx_stl_map_ext.so.0.0.1' g++ -o smtbx/refinement/boost_python/least_squares_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/boost_python/least_squares_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/refinement/boost_python/weighting_schemes.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/boost_python/weighting_schemes.cpp @@ -27715,8 +27751,8 @@ g++ -o smtbx/refinement/restraints/boost_python/restraints_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/restraints/boost_python/restraints_ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/stl/map_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/stl/map_ext.cpp -g++ -o smtbx/structure_factors/direct/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/structure_factors/direct/boost_python/ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o smtbx/structure_factors/direct/boost_python/ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/structure_factors/direct/boost_python/ext.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o smtbx/structure_factors/direct/boost_python/standard_xray.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/structure_factors/direct/boost_python/standard_xray.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ @@ -27747,6 +27783,8 @@ 'lib/std_pair_ext.so'->'lib/std_pair_ext.so.0.0.1' g++ -o mmtbx/masks/tst_mask.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/mmtbx/masks/tst_mask.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/array_family/boost_python/regression_test_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/smtbx_stl_map_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_stl_map_ext.so.0 smtbx/stl/map_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -27759,26 +27797,10 @@ Create symlinks for: 'lib/smtbx_stl_map_ext.so.0.0.1' 'lib/smtbx_stl_map_ext.so.0'->'lib/smtbx_stl_map_ext.so.0.0.1' 'lib/smtbx_stl_map_ext.so'->'lib/smtbx_stl_map_ext.so.0.0.1' -g++ -o scitbx/array_family/boost_python/regression_test_ext.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -DBOOST_PYTHON_MAX_BASES=2 -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/usr/include/python3.13 /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/array_family/tst_accessors.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_accessors.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o lib/spotfinder_hough_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=spotfinder_hough_ext.so.0 spotfinder/core_toolbox/boost_python/hough_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/spotfinder_hough_ext.so.0.0.1' - 'lib/spotfinder_hough_ext.so.0'->'lib/spotfinder_hough_ext.so.0.0.1' - 'lib/spotfinder_hough_ext.so'->'lib/spotfinder_hough_ext.so.0.0.1' g++ -o scitbx/array_family/tst_af_1.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_1.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/array_family/tst_af_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_2.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -27948,6 +27970,68 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_helpers.cpp:17:18: warning: comparison of integer expressions of different signedness: ‘const long int’ and ‘const long unsigned int’ [-Wsign-compare] 17 | if (v[i] != a[i]) { | ~~~~~^~~~~ +In file included from /usr/include/boost/assert.hpp:58, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:25, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/object.hpp:9, + from /usr/include/boost/python/list.hpp:10, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:7: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = std::vector; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = std::vector; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:156:78: required from here + 156 | scitbx::boost_python::container_conversions::variable_capacity_policy>(); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = std::__cxx11::list; ConversionPolicy = scitbx::boost_python::container_conversions::linked_list_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = std::__cxx11::list; ConversionPolicy = scitbx::boost_python::container_conversions::linked_list_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:160:72: required from here + 160 | scitbx::boost_python::container_conversions::linked_list_policy>(); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = boost::array; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_size_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = boost::array; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_size_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:164:71: required from here + 164 | scitbx::boost_python::container_conversions::fixed_size_policy>(); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = boost::array; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_size_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = boost::array; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_size_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:168:71: required from here + 168 | scitbx::boost_python::container_conversions::fixed_size_policy>(); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::small; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_capacity_policy; PyObject = _object]’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::small; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_capacity_policy]’ + 146 | &convertible, + | ^~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:172:75: required from here + 172 | scitbx::boost_python::container_conversions::fixed_capacity_policy>(); + | ^ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 197 | if (!is_range) assert(i == obj_size); + | ~~^~~~~~~~~~~ +g++ -o mmtbx/masks/tst_mask -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread mmtbx/masks/tst_mask.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lmmtbx_masks -liotbx_pdb -lcctbx -lomptbx -lcctbx_sgtbx_asu -lm In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include/scitbx/array_family/tiny_plain_apply.h:15, @@ -28167,6 +28251,22 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:59:15: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 59 | if (N < last - first) throw_range_error(); | ~~^~~~~~~~~~~~~~ +g++ -o scitbx/array_family/tst_af_2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_2.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/spotfinder_hough_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=spotfinder_hough_ext.so.0 spotfinder/core_toolbox/boost_python/hough_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/spotfinder_hough_ext.so.0.0.1' + 'lib/spotfinder_hough_ext.so.0'->'lib/spotfinder_hough_ext.so.0.0.1' + 'lib/spotfinder_hough_ext.so'->'lib/spotfinder_hough_ext.so.0.0.1' +g++ -o scitbx/array_family/tst_af_3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_3.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -28278,70 +28378,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o mmtbx/masks/tst_mask -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread mmtbx/masks/tst_mask.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lmmtbx_masks -liotbx_pdb -lcctbx -lomptbx -lcctbx_sgtbx_asu -lm -In file included from /usr/include/boost/assert.hpp:58, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:25, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object.hpp:9, - from /usr/include/boost/python/list.hpp:10, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:7: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = std::vector; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = std::vector; ConversionPolicy = scitbx::boost_python::container_conversions::variable_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:156:78: required from here - 156 | scitbx::boost_python::container_conversions::variable_capacity_policy>(); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = std::__cxx11::list; ConversionPolicy = scitbx::boost_python::container_conversions::linked_list_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = std::__cxx11::list; ConversionPolicy = scitbx::boost_python::container_conversions::linked_list_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:160:72: required from here - 160 | scitbx::boost_python::container_conversions::linked_list_policy>(); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = boost::array; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_size_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = boost::array; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_size_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:164:71: required from here - 164 | scitbx::boost_python::container_conversions::fixed_size_policy>(); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = boost::array; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_size_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = boost::array; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_size_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:168:71: required from here - 168 | scitbx::boost_python::container_conversions::fixed_size_policy>(); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h: In instantiation of ‘static void* scitbx::boost_python::container_conversions::from_python_sequence::convertible(PyObject*) [with ContainerType = scitbx::af::small; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_capacity_policy; PyObject = _object]’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:146:9: required from ‘scitbx::boost_python::container_conversions::from_python_sequence::from_python_sequence() [with ContainerType = scitbx::af::small; ConversionPolicy = scitbx::boost_python::container_conversions::fixed_capacity_policy]’ - 146 | &convertible, - | ^~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/boost_python/regression_test_ext.cpp:172:75: required from here - 172 | scitbx::boost_python::container_conversions::fixed_capacity_policy>(); - | ^ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/boost_python/container_conversions.h:197:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 197 | if (!is_range) assert(i == obj_size); - | ~~^~~~~~~~~~~ -g++ -o scitbx/array_family/tst_af_3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_3.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/simple_io.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_3.cpp:1: @@ -28452,6 +28488,9 @@ g++ -o scitbx/array_family/tst_af_2 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_af_2.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system g++ -o scitbx/array_family/tst_af_4.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_4.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/array_family/tst_accessors -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_accessors.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/array_family/tst_af_5.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_5.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/simple_io.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_4.cpp:1: @@ -28559,12 +28598,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_accessors -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_accessors.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -g++ -o scitbx/array_family/tst_af_5.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_5.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/array_family/tst_af_3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_af_3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -g++ -o scitbx/array_family/tst_mat3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_mat3.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/simple_io.h:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_af_5.cpp:1: @@ -28620,7 +28653,23 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_af_1 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_af_1.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/array_family/tst_af_3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_af_3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/array_family/tst_mat3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_mat3.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/spotfinder_dxtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=spotfinder_dxtbx_ext.so.0 spotfinder/dxtbx_toolbox/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -ldxtbxspotfinder -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +Create symlinks for: 'lib/spotfinder_dxtbx_ext.so.0.0.1' + 'lib/spotfinder_dxtbx_ext.so.0'->'lib/spotfinder_dxtbx_ext.so.0.0.1' + 'lib/spotfinder_dxtbx_ext.so'->'lib/spotfinder_dxtbx_ext.so.0.0.1' +g++ -o scitbx/array_family/tst_optional_copy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_optional_copy.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -28653,8 +28702,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_optional_copy.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_optional_copy.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -28767,16 +28814,11 @@ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o lib/smtbx_refinement_constraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_refinement_constraints_ext.so.0 smtbx/refinement/constraints/boost_python/affine.o smtbx/refinement/constraints/boost_python/constraints_ext.o smtbx/refinement/constraints/boost_python/direction.o smtbx/refinement/constraints/boost_python/geometrical_hydrogens.o smtbx/refinement/constraints/boost_python/independent_scalar_parameters.o smtbx/refinement/constraints/boost_python/occupancy.o smtbx/refinement/constraints/boost_python/reparametrisation.o smtbx/refinement/constraints/boost_python/rigid.o smtbx/refinement/constraints/boost_python/same_group.o smtbx/refinement/constraints/boost_python/scaled_adp.o smtbx/refinement/constraints/boost_python/scatterer_parameters.o smtbx/refinement/constraints/boost_python/shared.o smtbx/refinement/constraints/boost_python/special_position.o smtbx/refinement/constraints/boost_python/symmetry_equivalent.o smtbx/refinement/constraints/boost_python/u_eq_dependent_u_iso.o smtbx/refinement/constraints/boost_python/u_iso_dependent_u_iso.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o lib/spotfinder_dxtbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=spotfinder_dxtbx_ext.so.0 spotfinder/dxtbx_toolbox/ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -ldxtbxspotfinder -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o scitbx/array_family/tst_af_1 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_af_1.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/array_family/tst_rectangular_full_packed.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_rectangular_full_packed.cpp g++ -o scitbx/array_family/tst_af_5 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_af_5.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/array_family/tst_ref_matrix_facet.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_ref_matrix_facet.cpp /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -28785,14 +28827,7 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/spotfinder_dxtbx_ext.so.0.0.1' - 'lib/spotfinder_dxtbx_ext.so.0'->'lib/spotfinder_dxtbx_ext.so.0.0.1' - 'lib/spotfinder_dxtbx_ext.so'->'lib/spotfinder_dxtbx_ext.so.0.0.1' -g++ -o scitbx/array_family/tst_rectangular_full_packed.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_rectangular_full_packed.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/array_family/tst_ref_matrix_facet.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_ref_matrix_facet.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/array_family/tst_mat3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_mat3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/accessors/rectangular_full_packed.h:3, @@ -28849,8 +28884,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_sym_mat3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_sym_mat3.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -28910,9 +28943,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_rectangular_full_packed.cpp:53:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 53 | for(int j=0; j'lib/smtbx_refinement_constraints_ext.so.0.0.1' - 'lib/smtbx_refinement_constraints_ext.so'->'lib/smtbx_refinement_constraints_ext.so.0.0.1' +g++ -o scitbx/array_family/tst_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_optional_copy.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_ref_matrix_facet.cpp:1: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: @@ -28941,8 +28972,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_unsigned_float_arithmetic.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_unsigned_float_arithmetic.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/array_family/boost_python/regression_test_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=regression_test_ext.so.0 scitbx/array_family/boost_python/regression_test_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -lboost_numpy313 +Create symlinks for: 'lib/smtbx_refinement_constraints_ext.so.0.0.1' + 'lib/smtbx_refinement_constraints_ext.so.0'->'lib/smtbx_refinement_constraints_ext.so.0.0.1' + 'lib/smtbx_refinement_constraints_ext.so'->'lib/smtbx_refinement_constraints_ext.so.0.0.1' /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -29021,15 +29054,34 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h:161:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 161 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(versa_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_optional_copy -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_optional_copy.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -g++ -o scitbx/array_family/boost_python/regression_test_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=regression_test_ext.so.0 scitbx/array_family/boost_python/regression_test_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -lboost_numpy313 +/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/aarch64-linux-gnu/libboost_numpy313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. +g++ -o scitbx/array_family/tst_sym_mat3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_sym_mat3.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/array_family/tst_rectangular_full_packed -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_rectangular_full_packed.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/array_family/tst_mat3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_mat3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm +Create symlinks for: 'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1' + 'scitbx/array_family/boost_python/regression_test_ext.so.0'->'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1' + 'scitbx/array_family/boost_python/regression_test_ext.so'->'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1' +g++ -o scitbx/array_family/tst_unsigned_float_arithmetic.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_unsigned_float_arithmetic.cpp g++ -o scitbx/array_family/tst_vec3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/usr/include -Iscitbx/array_family -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_vec3.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/error/tst_error.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/error -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error/tst_error.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/fftpack/timing/fftpack_timer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/timing/fftpack_timer.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o lib/smtbx_refinement_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_refinement_restraints_ext.so.0 smtbx/refinement/restraints/boost_python/origin_fixing.o smtbx/refinement/restraints/boost_python/restraints_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_numpy313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -29068,12 +29120,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Create symlinks for: 'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1' - 'scitbx/array_family/boost_python/regression_test_ext.so.0'->'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1' - 'scitbx/array_family/boost_python/regression_test_ext.so'->'scitbx/array_family/boost_python/regression_test_ext.so.0.0.1' -g++ -o scitbx/error/tst_error.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/error -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/error/tst_error.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/fftpack/timing/fftpack_timer.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/timing/fftpack_timer.cpp +Create symlinks for: 'lib/smtbx_refinement_restraints_ext.so.0.0.1' + 'lib/smtbx_refinement_restraints_ext.so.0'->'lib/smtbx_refinement_restraints_ext.so.0.0.1' + 'lib/smtbx_refinement_restraints_ext.so'->'lib/smtbx_refinement_restraints_ext.so.0.0.1' +g++ -o scitbx/fftpack/timing/test0.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/timing/test0.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, @@ -29109,38 +29159,6 @@ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/vec3.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_vec3.cpp:2: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_unsigned_float_arithmetic -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_unsigned_float_arithmetic.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_types.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/factorization.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/complex_to_complex.h:4, @@ -29171,9 +29189,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/fftpack/timing/test0.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/timing/test0.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/error/tst_error -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/error/tst_error.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -29207,11 +29222,38 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/factorization.h:67:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::tiny_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 67 | for (i = 0; i < opt_factors.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_ref_matrix_facet -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_ref_matrix_facet.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -g++ -o scitbx/lbfgs/sdrive_fem.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable scitbx/lbfgs/sdrive_fem.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/lbfgs/tst_lbfgs.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgs/tst_lbfgs.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/vec3.h:4, + from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tst_vec3.cpp:2: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/error/tst_error -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/error/tst_error.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny.h:4, @@ -29246,7 +29288,8 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_vec3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_vec3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm +g++ -o scitbx/array_family/tst_ref_matrix_facet -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_ref_matrix_facet.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/lbfgs/sdrive_fem.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable scitbx/lbfgs/sdrive_fem.cpp /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -29273,6 +29316,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/array_family/tst_unsigned_float_arithmetic -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_unsigned_float_arithmetic.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/factorization.h: In constructor ‘scitbx::fftpack::factorization::factorization(std::size_t, bool)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/factorization.h:64:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::tiny_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 64 | for (i = 0; red_n > 1 && i < opt_factors.size(); i++) { @@ -29280,6 +29324,7 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/fftpack/factorization.h:67:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘scitbx::af::tiny_plain::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 67 | for (i = 0; i < opt_factors.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/versa_plain.h: In member function ‘ElementType& scitbx::af::versa_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -29332,6 +29377,10 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/lbfgs/tst_lbfgs.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgs/tst_lbfgs.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/lbfgsb/dev/driver1.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/dev/driver1.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/io.hpp:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/close_chain.hpp:4, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/common.hpp:4, @@ -29344,8 +29393,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/simple_streams.hpp:63:13: warning: comparison of integer expressions of different signedness: ‘fem::ssize_t’ {aka ‘long int’} and ‘fem::size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 63 | if (i < sz) s[i++] = c; | ~~^~~~ -g++ -o scitbx/lbfgsb/dev/driver1.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/dev/driver1.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/common.hpp: In member function ‘void fem::common::getarg(int, fem::str_ref) const’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/common.hpp:40:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 40 | if (pos < 0 || pos >= command_line_args.buffer.size()) { @@ -29360,7 +29407,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/read.hpp:653:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 653 | if (iw+1 != ed.size()) { | ~~~~~^~~~~~~~~~~~ -g++ -o scitbx/array_family/tst_sym_mat3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_sym_mat3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/variant.hpp:5, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/major_types.hpp:7: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/utils/equivalence.hpp: In member function ‘void fem::utils::equivalence::array_alignment::infer_diffs0_from_diff_matrix()’: @@ -29372,8 +29418,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/fable/fem/write.hpp:704:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 704 | while (pos < internal_file_len) { | ~~~~^~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/lbfgsb/dev/driver2.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/dev/driver2.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/raw.h:6, from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/dev/driver1.cpp:1: @@ -29635,6 +29679,16 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/raw.h:188:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 188 | for(int j=0;j::at(size_type)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -o scitbx/matrix/tests/tst_cholesky.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests/tst_cholesky.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 62 | if (i >= sz) throw_range_error(); return beg[i]; \ @@ -29697,7 +29808,32 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/lbfgs/sdrive_fem -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/lbfgs/sdrive_fem.o scitbx/lbfgs/lbfgs_fem.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(size_type) const’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ + 65 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] + 62 | if (i >= sz) throw_range_error(); return beg[i]; \ + | ^~ +/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ + 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 62 | if (i >= sz) throw_range_error(); return beg[i]; \ | ^~~~~~ @@ -29830,107 +29966,6 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/raw.h:3675:5: note: in expansion of macro ‘SCITBX_ASSERT’ 3675 | SCITBX_ASSERT(g.size() == n); | ^~~~~~~~~~~~~ -g++ -o lib/smtbx_refinement_restraints_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_refinement_restraints_ext.so.0 smtbx/refinement/restraints/boost_python/origin_fixing.o smtbx/refinement/restraints/boost_python/restraints_ext.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o scitbx/lbfgs/tst_lbfgs -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/lbfgs/tst_lbfgs.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm -g++ -o scitbx/lbfgsb/dev/driver3.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/dev/driver3.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -/usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o scitbx/math/tests/tst.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/math/tests -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/tests /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/math/tests/tst.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -Create symlinks for: 'lib/smtbx_refinement_restraints_ext.so.0.0.1' - 'lib/smtbx_refinement_restraints_ext.so.0'->'lib/smtbx_refinement_restraints_ext.so.0.0.1' - 'lib/smtbx_refinement_restraints_ext.so'->'lib/smtbx_refinement_restraints_ext.so.0.0.1' -g++ -o scitbx/matrix/tests/tst_cholesky.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests/tst_cholesky.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -In file included from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/ref.h:8, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/raw.h:6, - from /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/dev/driver3.cpp:1: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘ElementType& scitbx::af::tiny_plain::at(size_type)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h: In member function ‘const ElementType& scitbx::af::tiny_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/tiny_plain.h:48:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 48 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(tiny_plain, elems, N) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In member function ‘ElementType& scitbx::af::small_plain::at(size_type)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h: In member function ‘const ElementType& scitbx::af::small_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/small_plain.h:107:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 107 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(small_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘ElementType& scitbx::af::shared_plain::at(size_type)’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:62:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 62 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h: In member function ‘const ElementType& scitbx::af::shared_plain::at(size_type) const’: -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/detail/ref_helpers.h:65:37: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ - 65 | if (i >= sz) throw_range_error(); return beg[i]; \ - | ^~~~~~ -/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/array_family/shared_plain.h:277:7: note: in expansion of macro ‘SCITBX_ARRAY_FAMILY_BEGIN_END_ETC’ - 277 | SCITBX_ARRAY_FAMILY_BEGIN_END_ETC(shared_plain, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -o scitbx/fftpack/timing/fftpack_timer -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/fftpack/timing/fftpack_timer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lomptbx -lm /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/raw.h: In instantiation of ‘void scitbx::lbfgsb::raw::write_ref1(const std::string&, const ref1&, const char*) [with ElementType = double; std::string = std::__cxx11::basic_string]’: /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/dev/driver3.cpp:82:19: required from here 82 | write_ref1(" ", wa.get1(j+1,n)); @@ -30044,28 +30079,19 @@ /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/lbfgsb/raw.h:3675:5: note: in expansion of macro ‘SCITBX_ASSERT’ 3675 | SCITBX_ASSERT(g.size() == n); | ^~~~~~~~~~~~~ +g++ -o scitbx/fftpack/timing/fftpack_timer -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/fftpack/timing/fftpack_timer.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lomptbx -lm g++ -o scitbx/matrix/tests/tst_givens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests/tst_givens.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/math/tests/tst -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/math/tests/tst.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/fftpack/timing/test0 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/fftpack/timing/test0.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lomptbx -lm g++ -o scitbx/matrix/tests/tst_householder.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests/tst_householder.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/fftpack/timing/test0 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/fftpack/timing/test0.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -lomptbx -lm g++ -o scitbx/matrix/tests/tst_svd.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/matrix/tests -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/matrix/tests/tst_svd.cpp -g++ -o scitbx/matrix/tests/tst_givens -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/matrix/tests/tst_givens.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/lbfgsb/dev/driver1 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/lbfgsb/dev/driver1.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_timer -lboost_chrono -lm g++ -o scitbx/serialization/tst_base_256.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -Wall -Wno-unknown-pragmas -Wno-parentheses -Winit-self -Wno-unused-local-typedefs -Werror=vla -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/serialization -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/serialization /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/serialization/tst_base_256.cpp cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/sparse/tests/tst_sparse.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/sparse/tests -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/tests /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/tests/tst_sparse.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o scitbx/lbfgsb/dev/driver3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/lbfgsb/dev/driver3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_timer -lboost_chrono -lm -g++ -o scitbx/lbfgsb/dev/driver2 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/lbfgsb/dev/driver2.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_timer -lboost_chrono -lm -g++ -o smtbx/refinement/constraints/tests/tst_geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -g++ -o smtbx/refinement/constraints/tests/tst_reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/tests/tst_reparametrisation.cpp -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o lib/spotfinder_distltbx_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=spotfinder_distltbx_ext.so.0 spotfinder/core_toolbox/boost_python/distltbx_ext.o spotfinder/diffraction/geometry.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o scitbx/serialization/tst_base_256 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/serialization/tst_base_256.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -30074,14 +30100,26 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -g++ -o smtbx/refinement/constraints/tests/tst_special_position.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/tests/tst_special_position.cpp +g++ -o scitbx/matrix/tests/tst_givens -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/matrix/tests/tst_givens.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system Create symlinks for: 'lib/spotfinder_distltbx_ext.so.0.0.1' 'lib/spotfinder_distltbx_ext.so.0'->'lib/spotfinder_distltbx_ext.so.0.0.1' 'lib/spotfinder_distltbx_ext.so'->'lib/spotfinder_distltbx_ext.so.0.0.1' +g++ -o scitbx/sparse/tests/tst_sparse.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Iscitbx/sparse/tests -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/tests /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/scitbx/sparse/tests/tst_sparse.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o smtbx/refinement/constraints/tests/tst_geometrical_hydrogens.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o scitbx/lbfgsb/dev/driver3 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/lbfgsb/dev/driver3.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_timer -lboost_chrono -lm +g++ -o scitbx/lbfgsb/dev/driver2 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/lbfgsb/dev/driver2.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_timer -lboost_chrono -lm +g++ -o smtbx/refinement/constraints/tests/tst_reparametrisation.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/tests/tst_reparametrisation.cpp +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +g++ -o smtbx/refinement/constraints/tests/tst_special_position.o -c -g -O2 -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I/usr/include/hdf5/serial -DBOOST_TIMER_ENABLE_DEPRECATED=1 -std=c++14 -pthread -fPIC -fno-strict-aliasing -w -g -O0 -fno-inline -DBOOST_ALL_NO_LIB -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1 -I/usr/include -Ismtbx/refinement/constraints -I/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints /build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/refinement/constraints/tests/tst_special_position.cpp +g++ -o scitbx/serialization/tst_base_256 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/serialization/tst_base_256.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ g++ -o scitbx/matrix/tests/tst_cholesky -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/matrix/tests/tst_cholesky.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -g++ -o lib/smtbx_refinement_least_squares_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_refinement_least_squares_ext.so.0 smtbx/refinement/boost_python/least_squares_ext.o smtbx/refinement/boost_python/weighting_schemes.o smtbx/refinement/boost_python/least_squares.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm g++ -o scitbx/matrix/tests/tst_svd -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/matrix/tests/tst_svd.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o scitbx/matrix/tests/tst_householder -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/matrix/tests/tst_householder.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +g++ -o lib/smtbx_structure_factors_direct_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_structure_factors_direct_ext.so.0 smtbx/structure_factors/direct/boost_python/ext.o smtbx/structure_factors/direct/boost_python/standard_xray.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o scitbx/sparse/tests/tst_sparse -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/sparse/tests/tst_sparse.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -30090,12 +30128,11 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/smtbx_refinement_least_squares_ext.so.0.0.1' - 'lib/smtbx_refinement_least_squares_ext.so.0'->'lib/smtbx_refinement_least_squares_ext.so.0.0.1' - 'lib/smtbx_refinement_least_squares_ext.so'->'lib/smtbx_refinement_least_squares_ext.so.0.0.1' -g++ -o scitbx/matrix/tests/tst_householder -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/matrix/tests/tst_householder.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system -g++ -o lib/smtbx_structure_factors_direct_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_structure_factors_direct_ext.so.0 smtbx/structure_factors/direct/boost_python/ext.o smtbx/structure_factors/direct/boost_python/standard_xray.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm -g++ -o scitbx/sparse/tests/tst_sparse -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/sparse/tests/tst_sparse.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lboost_thread -lboost_system +Create symlinks for: 'lib/smtbx_structure_factors_direct_ext.so.0.0.1' + 'lib/smtbx_structure_factors_direct_ext.so.0'->'lib/smtbx_structure_factors_direct_ext.so.0.0.1' + 'lib/smtbx_structure_factors_direct_ext.so'->'lib/smtbx_structure_factors_direct_ext.so.0.0.1' +g++ -o smtbx/refinement/constraints/tests/tst_special_position -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread smtbx/refinement/constraints/tests/tst_special_position.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lsmtbx_refinement_constraints -lboost_thread -lboost_system +g++ -o lib/smtbx_refinement_least_squares_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=smtbx_refinement_least_squares_ext.so.0 smtbx/refinement/boost_python/least_squares_ext.o smtbx/refinement/boost_python/weighting_schemes.o smtbx/refinement/boost_python/least_squares.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lsmtbx_refinement_constraints -lscitbx_boost_python -lcctbx -lboost_thread -lboost_system -lboost_python313 -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -30104,14 +30141,13 @@ /lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. -Create symlinks for: 'lib/smtbx_structure_factors_direct_ext.so.0.0.1' - 'lib/smtbx_structure_factors_direct_ext.so.0'->'lib/smtbx_structure_factors_direct_ext.so.0.0.1' - 'lib/smtbx_structure_factors_direct_ext.so'->'lib/smtbx_structure_factors_direct_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/tests/tst_geometrical_hydrogens -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread smtbx/refinement/constraints/tests/tst_geometrical_hydrogens.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lsmtbx_refinement_constraints -lboost_thread -lboost_system -g++ -o smtbx/refinement/constraints/tests/tst_special_position -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread smtbx/refinement/constraints/tests/tst_special_position.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lsmtbx_refinement_constraints -lboost_thread -lboost_system +Create symlinks for: 'lib/smtbx_refinement_least_squares_ext.so.0.0.1' + 'lib/smtbx_refinement_least_squares_ext.so.0'->'lib/smtbx_refinement_least_squares_ext.so.0.0.1' + 'lib/smtbx_refinement_least_squares_ext.so'->'lib/smtbx_refinement_least_squares_ext.so.0.0.1' g++ -o smtbx/refinement/constraints/tests/tst_reparametrisation -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread smtbx/refinement/constraints/tests/tst_reparametrisation.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lcctbx -lsmtbx_refinement_constraints -lboost_thread -lboost_system -g++ -o scitbx/array_family/tst_af_4 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_af_4.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm g++ -o lib/spotfinder_array_family_flex_ext.so.0.0.1 -shared -rdynamic -std=c++14 -Wl,-soname=spotfinder_array_family_flex_ext.so.0 spotfinder/array_family/flex_ext.o spotfinder/array_family/flex_distl_spot.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lspotfinder -lomptbx -lscitbx_boost_python -lboost_thread -lboost_system -lboost_python313 -lm +g++ -o scitbx/array_family/tst_af_4 -rdynamic -Wl,-z,relro -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lhdf5 -std=c++14 -pthread scitbx/array_family/tst_af_4.o -L/usr/lib -L/usr/lib64 -L/usr/lib/aarch64-linux-gnu -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -Llib -L/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/lib -lm /usr/lib/aarch64-linux-gnu/libboost_thread.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_system.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /usr/lib/aarch64-linux-gnu/libboost_python313.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -30124,8 +30160,8 @@ 'lib/spotfinder_array_family_flex_ext.so.0'->'lib/spotfinder_array_family_flex_ext.so.0.0.1' 'lib/spotfinder_array_family_flex_ext.so'->'lib/spotfinder_array_family_flex_ext.so.0.0.1' scons: done building targets. -usr+sys time: 28.39 seconds -wall clock time: 19 minutes 12.57 seconds (1152.57 seconds total) +usr+sys time: 25.90 seconds +wall clock time: 7 minutes 19.82 seconds (439.82 seconds total) iconv -f ISO-8859-1 -t UTF-8 cctbx/eltbx/covalent_radii.h > covalent_radii.h mv covalent_radii.h cctbx/eltbx/covalent_radii.h # cp all extensions into the python build directory @@ -45530,6 +45566,7 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/rstbx.show_dist_paths"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/show_dist_paths.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/serialtbx.show_dist_paths"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/show_dist_paths.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/wxtbx.show_dist_paths"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/show_dist_paths.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/iotbx.fetch_pdb"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../mmtbx/command_line/fetch_pdb.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/phenix.fake_f_obs"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../mmtbx/command_line/fake_f_obs.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/phenix.fab_elbow_angle"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../mmtbx/command_line/fab_elbow_angle.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/phenix.f000"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../mmtbx/command_line/f000.py"), @@ -45741,7 +45778,6 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/phenix.find_peaks_holes"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../mmtbx/command_line/find_peaks_holes.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/mmtbx.find_peaks_holes"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../mmtbx/command_line/find_peaks_holes.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/phenix.fetch_pdb"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../mmtbx/command_line/fetch_pdb.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/iotbx.fetch_pdb"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../mmtbx/command_line/fetch_pdb.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/cctbx.HKLinfo"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../crys3d/command_line/HKLinfo.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/smtbx.refine"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../smtbx/command_line/refine.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/smtbx.masks"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../smtbx/command_line/masks.py"), @@ -45806,6 +45842,7 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/iotbx.file_reader"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../iotbx/command_line/file_reader.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/iotbx.export_scalepack_unmerged"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../iotbx/command_line/export_scalepack_unmerged.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/phenix.explore_metric_symmetry"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../iotbx/command_line/explore_metric_symmetry.py"), + relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.assert_stdin_contains_strings"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/assert_stdin_contains_strings.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.assert_stdin_does_not_contain_strings"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/assert_stdin_contains_strings.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.assert_stdin"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/assert_stdin.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.assert_not_show_diff"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/assert_not_show_diff.py"), @@ -45930,7 +45967,6 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.bibtex"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/bibtex.sh"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.bash"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/bash.sh"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.assert_stdin_ends_with"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/assert_stdin_ends_with.py"), - relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.assert_stdin_contains_strings"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/assert_stdin_contains_strings.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.python"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="/usr/bin/python3.13"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.wait_for_file"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/wait_for_file.py"), relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.valgrind"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/valgrind.sh"), @@ -45973,7 +46009,7 @@ relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin/libtbx.resource_monitor_plot"): relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/resource_monitor_plot.py")}, 'bin_path': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="bin"), 'boost_version': 108300, - 'build_options': , + 'build_options': , 'build_path': absolute_path("/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13"), 'command_line_redirections': {}, 'command_version_suffix': None, @@ -46010,30 +46046,30 @@ 'lib_path': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="lib"), 'missing_for_build': set(), 'missing_for_use': set(), - 'missing_optional': {'king', 'cbflib', 'probe', 'docutils', 'reduce'}, - 'module_dict': {'annlib': , - 'boost': , - 'cbflib': , - 'ccp4io': , - 'cctbx': , - 'chiltbx': , - 'cma_es': , - 'crys3d': , - 'dxtbx': , - 'fable': , - 'gltbx': , - 'iotbx': , - 'libtbx': , - 'mmtbx': , - 'omptbx': , - 'rstbx': , - 'scitbx': , - 'serialtbx': , - 'smtbx': , - 'spotfinder': , - 'tbxx': , - 'ucif': , - 'wxtbx': }, + 'missing_optional': {'cbflib', 'reduce', 'docutils', 'king', 'probe'}, + 'module_dict': {'annlib': , + 'boost': , + 'cbflib': , + 'ccp4io': , + 'cctbx': , + 'chiltbx': , + 'cma_es': , + 'crys3d': , + 'dxtbx': , + 'fable': , + 'gltbx': , + 'iotbx': , + 'libtbx': , + 'mmtbx': , + 'omptbx': , + 'rstbx': , + 'scitbx': , + 'serialtbx': , + 'smtbx': , + 'spotfinder': , + 'tbxx': , + 'ucif': , + 'wxtbx': }, 'module_dist_paths': {'annlib': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../annlib"), 'annlib_adaptbx': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../annlib_adaptbx"), 'boost': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../boost"), @@ -46060,29 +46096,29 @@ 'tbxx': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../tbxx"), 'ucif': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../ucif"), 'wxtbx': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../wxtbx")}, - 'module_list': [, - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - ], + 'module_list': [, + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + ], 'no_bin_python': False, 'path_utility': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="../../../libtbx/command_line/path_utility.py"), 'python_exe': relocatable_path(anchor="/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/debian/tmp/usr/lib/cctbx/python3.13", relocatable="/usr/bin/python3.13"), @@ -46102,7 +46138,8 @@ {'_dispatcher_include_at_start': [], '_dispatcher_include_before_command': [], '_dispatcher_precall_commands': None, - '_dispatcher_registry': {relocatable_path(anchor="/usr", relocatable="bin/scitbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), + '_dispatcher_registry': {relocatable_path(anchor="/usr", relocatable="bin/fable.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), + relocatable_path(anchor="/usr", relocatable="bin/scitbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), relocatable_path(anchor="/usr", relocatable="bin/annlib.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), relocatable_path(anchor="/usr", relocatable="bin/cbflib.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), relocatable_path(anchor="/usr", relocatable="bin/ccp4io.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), @@ -46235,7 +46272,6 @@ relocatable_path(anchor="/usr", relocatable="bin/boost.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), relocatable_path(anchor="/usr", relocatable="bin/omptbx.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), relocatable_path(anchor="/usr", relocatable="bin/cma_es.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), - relocatable_path(anchor="/usr", relocatable="bin/fable.python"): relocatable_path(anchor="/usr", relocatable="bin/python3.13"), relocatable_path(anchor="/usr", relocatable="bin/phenix.reciprocal_space_arrays"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/reciprocal_space_arrays.py"), relocatable_path(anchor="/usr", relocatable="bin/mmtbx.rebuild_rotarama_cache"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/rebuild_rotarama_cache.py"), relocatable_path(anchor="/usr", relocatable="bin/mmtbx.rebuild_cablam_cache"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/mmtbx/command_line/rebuild_cablam_cache.py"), @@ -46320,7 +46356,7 @@ relocatable_path(anchor="/usr", relocatable="bin/sphinx.build"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/sphinx_build.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_variable_names"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_variable_names.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_tests"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_tests.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_repository_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_repository_paths.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_pythonpath"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_pythonpath.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_python_sys_executable"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_python_sys_executable.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_python_dependencies"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_python_dependencies.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_numpy_version"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_numpy_version.py"), @@ -46331,8 +46367,8 @@ relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_include_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_include_paths.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_host_and_user"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_host_and_user.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_full_command_path"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_full_command_path.py"), + relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_repository_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_repository_paths.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_environ_usage"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_environ_usage.py"), - relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_pythonpath"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_pythonpath.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_env"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_env.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_dist_paths"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_dist_paths.py"), relocatable_path(anchor="/usr", relocatable="bin/libtbx.show_date_and_time"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/show_date_and_time.py"), @@ -46617,7 +46653,7 @@ relocatable_path(anchor="/usr", relocatable="bin/libtbx.valgrind"): relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/valgrind.sh")}, 'bin_path': relocatable_path(anchor="/usr", relocatable="bin"), 'boost_version': 108300, - 'build_options': , + 'build_options': , 'build_path': absolute_path("/usr/lib/cctbx/python3.13"), 'command_line_redirections': {}, 'command_version_suffix': None, @@ -46654,30 +46690,30 @@ 'lib_path': relocatable_path(anchor="/usr", relocatable="lib"), 'missing_for_build': set(), 'missing_for_use': set(), - 'missing_optional': {'king', 'cbflib', 'probe', 'docutils', 'reduce'}, - 'module_dict': {'annlib': , - 'boost': , - 'cbflib': , - 'ccp4io': , - 'cctbx': , - 'chiltbx': , - 'cma_es': , - 'crys3d': , - 'dxtbx': , - 'fable': , - 'gltbx': , - 'iotbx': , - 'libtbx': , - 'mmtbx': , - 'omptbx': , - 'rstbx': , - 'scitbx': , - 'serialtbx': , - 'smtbx': , - 'spotfinder': , - 'tbxx': , - 'ucif': , - 'wxtbx': }, + 'missing_optional': {'cbflib', 'reduce', 'docutils', 'king', 'probe'}, + 'module_dict': {'annlib': , + 'boost': , + 'cbflib': , + 'ccp4io': , + 'cctbx': , + 'chiltbx': , + 'cma_es': , + 'crys3d': , + 'dxtbx': , + 'fable': , + 'gltbx': , + 'iotbx': , + 'libtbx': , + 'mmtbx': , + 'omptbx': , + 'rstbx': , + 'scitbx': , + 'serialtbx': , + 'smtbx': , + 'spotfinder': , + 'tbxx': , + 'ucif': , + 'wxtbx': }, 'module_dist_paths': {'annlib': relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/annlib"), 'annlib_adaptbx': relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/annlib_adaptbx"), 'boost': relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/boost"), @@ -46704,29 +46740,29 @@ 'tbxx': relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/tbxx"), 'ucif': relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/ucif"), 'wxtbx': relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/wxtbx")}, - 'module_list': [, - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - ], + 'module_list': [, + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + , + ], 'no_bin_python': True, 'path_utility': relocatable_path(anchor="/usr", relocatable="lib/python3/dist-packages/libtbx/command_line/path_utility.py"), 'python_exe': relocatable_path(anchor="/usr", relocatable="bin/python3.13"), @@ -46781,7 +46817,7 @@ smtbx/refinement/constraints/tests/tst_reparametrisation smtbx/refinement/constraints/tests/tst_special_position -sent 16,524,085 bytes received 568 bytes 11,016,435.33 bytes/sec +sent 16,524,097 bytes received 568 bytes 33,049,330.00 bytes/sec total size is 16,512,448 speedup is 1.00 building file list ... done ./ @@ -46843,13 +46879,13 @@ libspotfinder.so.0 -> libspotfinder.so.0.0.1 libspotfinder.so.0.0.1 -sent 56,668,576 bytes received 494 bytes 22,667,628.00 bytes/sec +sent 56,668,567 bytes received 494 bytes 113,338,122.00 bytes/sec total size is 56,652,474 speedup is 1.00 building file list ... done annlib_adaptbx/ annlib_adaptbx/ann_adaptor.h -sent 2,232 bytes received 38 bytes 4,540.00 bytes/sec +sent 2,234 bytes received 38 bytes 4,544.00 bytes/sec total size is 2,068 speedup is 0.91 building file list ... done boost_adaptbx/ @@ -46875,7 +46911,7 @@ boost_adaptbx/tests/ boost_adaptbx/tests/tst_optional_copy.h -sent 73,852 bytes received 386 bytes 148,476.00 bytes/sec +sent 73,856 bytes received 386 bytes 148,484.00 bytes/sec total size is 72,301 speedup is 0.97 building file list ... done cbflib_adaptbx/ @@ -46889,7 +46925,7 @@ cbflib_adaptbx/detectors/boost_python/cbf_binary_adaptor.h cbflib_adaptbx/detectors/boost_python/general_cbf_write.h -sent 22,312 bytes received 158 bytes 44,940.00 bytes/sec +sent 22,313 bytes received 158 bytes 44,942.00 bytes/sec total size is 21,627 speedup is 0.96 building file list ... done ccp4io_adaptbx/ @@ -46911,7 +46947,7 @@ ccp4io_adaptbx/dev/ ccp4io_adaptbx/dev/fftlib.hpp -sent 87,920 bytes received 326 bytes 176,492.00 bytes/sec +sent 87,940 bytes received 326 bytes 176,532.00 bytes/sec total size is 86,683 speedup is 0.98 building file list ... done cctbx/ @@ -47171,7 +47207,7 @@ cctbx/xray/targets/mli.h cctbx/xray/targets/shelxl_wght_ls.hpp -sent 1,904,538 bytes received 4,420 bytes 3,817,916.00 bytes/sec +sent 1,904,561 bytes received 4,420 bytes 3,817,962.00 bytes/sec total size is 1,887,892 speedup is 0.99 building file list ... done cma_es/ @@ -47179,7 +47215,7 @@ cma_es/cma/cmaes.h cma_es/cma/cmaes_interface.h -sent 6,892 bytes received 60 bytes 13,904.00 bytes/sec +sent 6,888 bytes received 60 bytes 13,896.00 bytes/sec total size is 6,671 speedup is 0.96 building file list ... done @@ -47225,7 +47261,7 @@ dxtbx/model/boost_python/pickle_suite.h dxtbx/model/boost_python/to_from_dict.h -sent 396,148 bytes received 610 bytes 793,516.00 bytes/sec +sent 396,151 bytes received 610 bytes 264,507.33 bytes/sec total size is 393,719 speedup is 0.99 building file list ... done ./ @@ -47279,7 +47315,7 @@ fem/utils/string_to_double_fmt.hpp fem/utils/token.hpp -sent 203,950 bytes received 918 bytes 409,736.00 bytes/sec +sent 203,962 bytes received 918 bytes 409,760.00 bytes/sec total size is 200,764 speedup is 0.98 building file list ... done gltbx/ @@ -47293,7 +47329,7 @@ gltbx/special_wrapper_support.h gltbx/util.h -sent 598,784 bytes received 190 bytes 1,197,948.00 bytes/sec +sent 598,790 bytes received 190 bytes 1,197,960.00 bytes/sec total size is 597,954 speedup is 1.00 building file list ... done iotbx/ @@ -47336,11 +47372,11 @@ iotbx/xplor/map_reader.h iotbx/xplor/map_writer.h -sent 270,340 bytes received 629 bytes 180,646.00 bytes/sec +sent 270,336 bytes received 629 bytes 541,930.00 bytes/sec total size is 267,526 speedup is 0.99 building file list ... done -sent 455 bytes received 12 bytes 934.00 bytes/sec +sent 482 bytes received 12 bytes 988.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done mmtbx/ @@ -47433,7 +47469,7 @@ mmtbx/validation/ramachandran/rama8000_tables.h mmtbx/validation/ramachandran/rama_eval.h -sent 2,052,487 bytes received 1,291 bytes 4,107,556.00 bytes/sec +sent 2,052,491 bytes received 1,291 bytes 4,107,564.00 bytes/sec total size is 2,046,334 speedup is 1.00 building file list ... done omptbx/ @@ -47477,7 +47513,7 @@ rstbx/symmetry/constraints/ rstbx/symmetry/constraints/a_g_conversion.h -sent 111,333 bytes received 400 bytes 223,466.00 bytes/sec +sent 111,334 bytes received 400 bytes 223,468.00 bytes/sec total size is 109,476 speedup is 0.98 building file list ... done scitbx/ @@ -47800,7 +47836,7 @@ scitbx/wigner/ scitbx/wigner/wigner3j.h -sent 1,905,853 bytes received 5,521 bytes 3,822,748.00 bytes/sec +sent 1,905,873 bytes received 5,521 bytes 3,822,788.00 bytes/sec total size is 1,886,121 speedup is 0.99 building file list ... done @@ -47840,7 +47876,7 @@ smtbx/structure_factors/direct/standard_xray.h smtbx/structure_factors/direct/table_based.h -sent 182,121 bytes received 512 bytes 365,266.00 bytes/sec +sent 182,136 bytes received 512 bytes 365,296.00 bytes/sec total size is 179,686 speedup is 0.98 building file list ... done spotfinder/ @@ -47859,7 +47895,7 @@ spotfinder/dxtbx_toolbox/distl.h spotfinder/dxtbx_toolbox/libdistl.h -sent 42,933 bytes received 221 bytes 86,308.00 bytes/sec +sent 42,932 bytes received 221 bytes 86,306.00 bytes/sec total size is 41,966 speedup is 0.97 building file list ... done tbxx/ @@ -47880,8 +47916,10 @@ ./ boost_adaptbx/ boost_adaptbx/type_id_eq.h +cctbx/ cctbx/boost_python/ cctbx/boost_python/flex_fwd.h +scitbx/ scitbx/lbfgs_fem.hpp scitbx/array_family/ scitbx/array_family/operator_traits_builtin.h @@ -47908,38 +47946,39 @@ scitbx/array_family/detail/ scitbx/array_family/detail/operator_functors.h scitbx/array_family/detail/std_imports.h +smtbx/ smtbx/boost_python/ smtbx/boost_python/flex_fwd.h -sent 347,298 bytes received 531 bytes 695,658.00 bytes/sec +sent 347,319 bytes received 540 bytes 695,718.00 bytes/sec total size is 345,070 speedup is 0.99 building file list ... done -sent 248 bytes received 12 bytes 520.00 bytes/sec +sent 256 bytes received 12 bytes 536.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done boost_adaptbx/ boost_adaptbx/command_line/ -sent 513 bytes received 22 bytes 1,070.00 bytes/sec -total size is 6,883 speedup is 12.87 +sent 554 bytes received 55 bytes 1,218.00 bytes/sec +total size is 6,883 speedup is 11.30 building file list ... done cbflib_adaptbx/ cbflib_adaptbx/command_line/ -sent 230 bytes received 22 bytes 504.00 bytes/sec -total size is 1,215 speedup is 4.82 +sent 237 bytes received 28 bytes 530.00 bytes/sec +total size is 1,215 speedup is 4.58 building file list ... done -sent 145 bytes received 12 bytes 314.00 bytes/sec +sent 149 bytes received 12 bytes 322.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done cctbx/ cctbx/command_line/ cctbx/command_line/web.install.csh -sent 3,000 bytes received 41 bytes 6,082.00 bytes/sec -total size is 39,666 speedup is 13.04 +sent 3,075 bytes received 101 bytes 6,352.00 bytes/sec +total size is 39,666 speedup is 12.49 building file list ... done sent 87 bytes received 12 bytes 198.00 bytes/sec @@ -47948,32 +47987,32 @@ crys3d/ crys3d/command_line/ -sent 468 bytes received 22 bytes 980.00 bytes/sec -total size is 31,515 speedup is 64.32 +sent 498 bytes received 52 bytes 1,100.00 bytes/sec +total size is 31,515 speedup is 57.30 building file list ... done dxtbx/ dxtbx/command_line/ -sent 861 bytes received 22 bytes 1,766.00 bytes/sec -total size is 82,029 speedup is 92.90 +sent 920 bytes received 82 bytes 2,004.00 bytes/sec +total size is 82,029 speedup is 81.87 building file list ... done fable/ fable/command_line/ -sent 458 bytes received 22 bytes 960.00 bytes/sec -total size is 15,542 speedup is 32.38 +sent 487 bytes received 43 bytes 1,060.00 bytes/sec +total size is 15,542 speedup is 29.32 building file list ... done gltbx/ gltbx/command_line/ -sent 175 bytes received 22 bytes 394.00 bytes/sec -total size is 606 speedup is 3.08 +sent 195 bytes received 28 bytes 446.00 bytes/sec +total size is 606 speedup is 2.72 building file list ... done iotbx/ iotbx/command_line/ -sent 2,630 bytes received 22 bytes 5,304.00 bytes/sec -total size is 240,936 speedup is 90.85 +sent 2,848 bytes received 244 bytes 6,184.00 bytes/sec +total size is 240,936 speedup is 77.92 building file list ... done libtbx/ libtbx/command_line/ @@ -47994,8 +48033,8 @@ libtbx/command_line/unpack_in_sources.csh libtbx/command_line/valgrind.sh -sent 6,889 bytes received 329 bytes 14,436.00 bytes/sec -total size is 175,321 speedup is 24.29 +sent 7,201 bytes received 614 bytes 15,630.00 bytes/sec +total size is 175,321 speedup is 22.43 building file list ... done mmtbx/ mmtbx/command_line/ @@ -48003,8 +48042,8 @@ mmtbx/regression/command_line/ mmtbx/regression/command_line/tst_find_residue_in_pdb.py -sent 4,693 bytes received 47 bytes 9,480.00 bytes/sec -total size is 708,795 speedup is 149.53 +sent 5,058 bytes received 416 bytes 10,948.00 bytes/sec +total size is 708,795 speedup is 129.48 building file list ... done sent 76 bytes received 12 bytes 176.00 bytes/sec @@ -48013,8 +48052,8 @@ rstbx/ rstbx/command_line/ -sent 751 bytes received 22 bytes 1,546.00 bytes/sec -total size is 11,108 speedup is 14.37 +sent 779 bytes received 49 bytes 1,656.00 bytes/sec +total size is 11,108 speedup is 13.42 building file list ... done scitbx/ scitbx/command_line/ @@ -48025,7 +48064,7 @@ scitbx/command_line/show_sizes.py scitbx/command_line/unicode_examples.py -sent 11,671 bytes received 136 bytes 23,614.00 bytes/sec +sent 11,707 bytes received 136 bytes 23,686.00 bytes/sec total size is 9,958 speedup is 0.84 building file list ... done @@ -48035,14 +48074,14 @@ smtbx/ smtbx/command_line/ -sent 872 bytes received 22 bytes 1,788.00 bytes/sec -total size is 37,436 speedup is 41.87 +sent 909 bytes received 40 bytes 1,898.00 bytes/sec +total size is 37,436 speedup is 39.45 building file list ... done spotfinder/ spotfinder/command_line/ -sent 518 bytes received 22 bytes 1,080.00 bytes/sec -total size is 22,750 speedup is 42.13 +sent 542 bytes received 43 bytes 1,170.00 bytes/sec +total size is 22,750 speedup is 38.89 building file list ... done sent 87 bytes received 12 bytes 198.00 bytes/sec @@ -48051,11 +48090,11 @@ wxtbx/ wxtbx/command_line/ -sent 453 bytes received 22 bytes 950.00 bytes/sec -total size is 16,078 speedup is 33.85 +sent 485 bytes received 58 bytes 1,086.00 bytes/sec +total size is 16,078 speedup is 29.61 building file list ... done -sent 248 bytes received 12 bytes 520.00 bytes/sec +sent 256 bytes received 12 bytes 536.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done boost_adaptbx/graph/ @@ -48088,21 +48127,21 @@ boost_adaptbx/tests/tst_swig_args.py boost_adaptbx/tests/tst_tuple.py -sent 91,616 bytes received 515 bytes 184,262.00 bytes/sec +sent 91,624 bytes received 515 bytes 184,278.00 bytes/sec total size is 89,657 speedup is 0.97 building file list ... done cbflib_adaptbx/detectors/ cbflib_adaptbx/detectors/tst_memory.cpp -sent 1,213 bytes received 34 bytes 2,494.00 bytes/sec +sent 1,210 bytes received 34 bytes 2,488.00 bytes/sec total size is 967 speedup is 0.78 building file list ... done ccp4io_adaptbx/ ccp4io_adaptbx/dev/ ccp4io_adaptbx/dev/tst_fftlib.py -sent 7,594 bytes received 44 bytes 15,276.00 bytes/sec -total size is 9,205 speedup is 1.21 +sent 7,600 bytes received 44 bytes 15,288.00 bytes/sec +total size is 9,205 speedup is 1.20 building file list ... done cctbx/adp_restraints/ cctbx/adptbx/ @@ -48196,21 +48235,21 @@ cctbx/xray/observations/ cctbx/xray/targets/ -sent 464,781 bytes received 977 bytes 931,516.00 bytes/sec -total size is 2,082,452 speedup is 4.47 +sent 465,171 bytes received 1,352 bytes 311,015.33 bytes/sec +total size is 2,082,452 speedup is 4.46 building file list ... done cma_es/ -sent 118 bytes received 19 bytes 274.00 bytes/sec -total size is 3,008 speedup is 21.96 +sent 121 bytes received 22 bytes 286.00 bytes/sec +total size is 3,008 speedup is 21.03 building file list ... done crys3d/regression/ -sent 355 bytes received 15 bytes 740.00 bytes/sec -total size is 41,841 speedup is 113.08 +sent 373 bytes received 33 bytes 812.00 bytes/sec +total size is 41,841 speedup is 103.06 building file list ... done -sent 675 bytes received 12 bytes 1,374.00 bytes/sec +sent 691 bytes received 12 bytes 1,406.00 bytes/sec total size is 0 speedup is 0.00 building file list ... done fable/test/ @@ -48219,12 +48258,12 @@ fable/test/tst_separate_files.py fable/test/tst_show_calls.py -sent 12,858 bytes received 91 bytes 25,898.00 bytes/sec -total size is 151,869 speedup is 11.73 +sent 12,877 bytes received 106 bytes 25,966.00 bytes/sec +total size is 151,869 speedup is 11.70 building file list ... done -sent 204 bytes received 12 bytes 432.00 bytes/sec -total size is 8,108 speedup is 37.54 +sent 222 bytes received 24 bytes 492.00 bytes/sec +total size is 8,108 speedup is 32.96 building file list ... done iotbx/bioinformatics/ iotbx/bioinformatics/test/ @@ -48274,14 +48313,14 @@ iotbx/xds/tests/tst_xparm.py iotbx/xplor/ -sent 275,746 bytes received 541 bytes 552,574.00 bytes/sec -total size is 2,463,857 speedup is 8.92 +sent 276,159 bytes received 958 bytes 554,234.00 bytes/sec +total size is 2,463,857 speedup is 8.89 building file list ... done libtbx/phil/ libtbx/queuing_system_utils/ -sent 1,109 bytes received 18 bytes 2,254.00 bytes/sec -total size is 252,704 speedup is 224.23 +sent 1,214 bytes received 108 bytes 2,644.00 bytes/sec +total size is 252,704 speedup is 191.15 building file list ... done mmtbx/atomic_environment_vectors/ mmtbx/building/ @@ -48374,13 +48413,13 @@ mmtbx/validation/regression/ mmtbx/wwpdb/ -sent 817,891 bytes received 930 bytes 1,637,642.00 bytes/sec -total size is 7,316,132 speedup is 8.93 +sent 819,010 bytes received 2,049 bytes 1,642,118.00 bytes/sec +total size is 7,316,132 speedup is 8.91 building file list ... done omptbx/ -sent 97 bytes received 19 bytes 232.00 bytes/sec -total size is 1,175 speedup is 10.13 +sent 100 bytes received 22 bytes 244.00 bytes/sec +total size is 1,175 speedup is 9.63 building file list ... done rstbx/bpcx/ rstbx/bpcx/detector_model/ @@ -48394,8 +48433,8 @@ rstbx/sublattice_support/ rstbx/viewer/ -sent 1,007 bytes received 45 bytes 2,104.00 bytes/sec -total size is 179,407 speedup is 170.54 +sent 1,046 bytes received 87 bytes 2,266.00 bytes/sec +total size is 179,407 speedup is 158.35 building file list ... done scitbx/array_family/ scitbx/array_family/tst_accessors.cpp @@ -48502,8 +48541,8 @@ scitbx/tests/tst_smoothing.py scitbx/wigner/ -sent 678,665 bytes received 1,368 bytes 453,355.33 bytes/sec -total size is 1,112,037 speedup is 1.64 +sent 678,883 bytes received 1,566 bytes 1,360,898.00 bytes/sec +total size is 1,112,037 speedup is 1.63 building file list ... done sent 152 bytes received 12 bytes 328.00 bytes/sec @@ -48539,14 +48578,14 @@ smtbx/tests/ smtbx/tests/tst_utils.py -sent 144,551 bytes received 291 bytes 289,684.00 bytes/sec +sent 144,594 bytes received 327 bytes 289,842.00 bytes/sec total size is 248,243 speedup is 1.71 building file list ... done spotfinder/core_toolbox/ spotfinder/core_toolbox/boost_python/ spotfinder/core_toolbox/boost_python/tst_small_image.py -sent 5,475 bytes received 37 bytes 11,024.00 bytes/sec +sent 5,474 bytes received 37 bytes 11,022.00 bytes/sec total size is 5,074 speedup is 0.92 building file list ... done tbxx/ @@ -49038,7 +49077,7 @@ smtbx/regression/test_data/thpp.hkl smtbx/regression/test_data/thpp.ins -sent 5,029,165 bytes received 8,885 bytes 10,076,100.00 bytes/sec +sent 5,030,279 bytes received 8,885 bytes 3,359,442.67 bytes/sec total size is 4,971,820 speedup is 0.99 make[1]: Leaving directory '/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1' dh_install -O--buildsystem=pybuild @@ -49060,15 +49099,15 @@ install -m0755 -d debian/python3-cctbx/usr/share/doc/python3-cctbx install -p -m0644 debian/copyright debian/python3-cctbx/usr/share/doc/python3-cctbx/copyright dh_installchangelogs -O--buildsystem=pybuild + install -m0755 -d debian/libcctbx0/usr/share/doc/libcctbx0 + install -p -m0644 debian/.debhelper/generated/libcctbx0/dh_installchangelogs.dch.trimmed debian/libcctbx0/usr/share/doc/libcctbx0/changelog.Debian + install -p -m0644 ./CHANGELOG.rst debian/libcctbx0/usr/share/doc/libcctbx0/changelog install -m0755 -d debian/python3-cctbx/usr/share/doc/python3-cctbx install -p -m0644 debian/.debhelper/generated/python3-cctbx/dh_installchangelogs.dch.trimmed debian/python3-cctbx/usr/share/doc/python3-cctbx/changelog.Debian install -p -m0644 ./CHANGELOG.rst debian/python3-cctbx/usr/share/doc/python3-cctbx/changelog install -m0755 -d debian/libcctbx-dev/usr/share/doc/libcctbx-dev install -p -m0644 debian/.debhelper/generated/libcctbx-dev/dh_installchangelogs.dch.trimmed debian/libcctbx-dev/usr/share/doc/libcctbx-dev/changelog.Debian install -p -m0644 ./CHANGELOG.rst debian/libcctbx-dev/usr/share/doc/libcctbx-dev/changelog - install -m0755 -d debian/libcctbx0/usr/share/doc/libcctbx0 - install -p -m0644 debian/.debhelper/generated/libcctbx0/dh_installchangelogs.dch.trimmed debian/libcctbx0/usr/share/doc/libcctbx0/changelog.Debian - install -p -m0644 ./CHANGELOG.rst debian/libcctbx0/usr/share/doc/libcctbx0/changelog dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:180: version: 6.20250414 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] @@ -49769,7 +49808,7 @@ D: dh_python3 tools:101: fix_shebang (debian/python3-cctbx/usr/bin/annlib.show_dist_paths): doesn't look like a shebang: #! /bin/sh D: dh_python3 tools:101: fix_shebang (debian/python3-cctbx/usr/bin/annlib.show_build_path): doesn't look like a shebang: #! /bin/sh D: dh_python3 tools:101: fix_shebang (debian/python3-cctbx/usr/bin/annlib.python): doesn't look like a shebang: #! /bin/sh -D: dh_python3 fs:338: package python3-cctbx details = {'requires.txt': {'debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx-2023.12.egg-info/requires.txt'}, 'egg-info': {'debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx-3.23.0.egg-info/PKG-INFO', 'debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx-2023.12.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.13')}, 'ext_no_version': set()} +D: dh_python3 fs:338: package python3-cctbx details = {'requires.txt': {'debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx-2023.12.egg-info/requires.txt'}, 'egg-info': {'debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx-2023.12.egg-info/PKG-INFO', 'debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx-3.23.0.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.13')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-cctbx D: dh_python3 pydist:175: trying to find dependency for PIL (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed @@ -49822,7 +49861,7 @@ D: dh_python3 pydist:175: trying to find dependency for wxPython (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:284: dependency: included in build-deps -D: dh_python3 depends:253: D={'python3-hdf5plugin', 'python3 (>= 3.13~)', 'python3-ordered-set', 'python3-requests', 'python3-h5py (>= 3)', 'python3 (<< 3.14)', 'python3-wxgtk4.0', 'python3:any', 'python3-six', 'python3-numpy', 'python3-mrcfile', 'python3-procrunner', 'python3-pint', 'python3-matplotlib', 'python3-pil', 'python3-natsort', 'python3-nxmx', 'python3-pymol', 'python3-tqdm', 'python3-scipy'}; R=[]; S=[]; E=[], B=[]; RT=[] +D: dh_python3 depends:253: D={'python3-procrunner', 'python3-wxgtk4.0', 'python3-pymol', 'python3-h5py (>= 3)', 'python3-pil', 'python3-scipy', 'python3 (>= 3.13~)', 'python3-nxmx', 'python3-hdf5plugin', 'python3-matplotlib', 'python3-mrcfile', 'python3-natsort', 'python3-tqdm', 'python3:any', 'python3 (<< 3.14)', 'python3-ordered-set', 'python3-pint', 'python3-requests', 'python3-numpy', 'python3-six'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild install -m0755 -d debian/python3-cctbx/usr/share/lintian/overrides @@ -49878,17 +49917,17 @@ make[1]: Leaving directory '/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1' dh_strip_nondeterminism -O--buildsystem=pybuild Using 1761327529 as canonical time - Normalizing debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/ebi_blast.xml.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/ncbi_blast.xml.gz using File::StripNondeterminism::handlers::gzip + Normalizing debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx/bioinformatics/test/ebi_blast.xml.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--buildsystem=pybuild + cd debian/libcctbx0 cd debian/libcctbx-dev cd debian/python3-cctbx - cd debian/libcctbx0 - chmod a-x usr/share/doc/libcctbx-dev/changelog usr/share/doc/libcctbx-dev/changelog.Debian chmod a-x usr/share/doc/libcctbx0/changelog usr/share/doc/libcctbx0/changelog.Debian + chmod a-x usr/share/doc/libcctbx-dev/changelog usr/share/doc/libcctbx-dev/changelog.Debian + chmod a-x usr/share/doc/python3-cctbx/changelog usr/share/doc/python3-cctbx/changelog.Debian gzip -9nf usr/share/doc/libcctbx-dev/changelog usr/share/doc/libcctbx-dev/changelog.Debian gzip -9nf usr/share/doc/libcctbx0/changelog usr/share/doc/libcctbx0/changelog.Debian - chmod a-x usr/share/doc/python3-cctbx/changelog usr/share/doc/python3-cctbx/changelog.Debian gzip -9nf usr/share/doc/python3-cctbx/changelog usr/share/doc/python3-cctbx/changelog.Debian cd '/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1' cd '/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1' @@ -49898,10 +49937,10 @@ find debian/libcctbx-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-cctbx ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libcctbx0/usr/share/doc -type f -a -true -a ! -regex 'debian/libcctbx0/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libcctbx-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libcctbx-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libcctbx0/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libcctbx-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/libcctbx-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libcctbx-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libcctbx0 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libcctbx-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libcctbx0/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libcctbx-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libcctbx-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 @@ -49930,6 +49969,8 @@ objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/35/b8d88d46ce42e23b0e342eb1b5385ae44be197.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/11 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_pdb.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/11/8ec818e2a8aef469e456320fff8e209a5c6203.debug + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/86 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/86/5a085490aceeef108483d6c6a0f36caf1476ca.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/11/8ec818e2a8aef469e456320fff8e209a5c6203.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_pdb.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/11/8ec818e2a8aef469e456320fff8e209a5c6203.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_pdb.so.0.0.1 @@ -49945,8 +49986,6 @@ objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/16/0eee3a0a79ac061fdc3a16ead64b169795f1c2.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libspotfinder.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/cc objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/cc/25063d831d6cfb11fc27d15fdbe86e8184983b.debug - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/86 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/86/5a085490aceeef108483d6c6a0f36caf1476ca.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/cc/25063d831d6cfb11fc27d15fdbe86e8184983b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/cc/25063d831d6cfb11fc27d15fdbe86e8184983b.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 @@ -49955,21 +49994,21 @@ chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/44/c050ca42aedecee4c12dc3e9a3ff17790bae32.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/librstbx.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/44/c050ca42aedecee4c12dc3e9a3ff17790bae32.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/librstbx.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/41 - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_minpack.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/41/84449d13b44fd3e2a5697e24e6277267794cf1.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/41/84449d13b44fd3e2a5697e24e6277267794cf1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_minpack.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/41/84449d13b44fd3e2a5697e24e6277267794cf1.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_minpack.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0d - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_slatec.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0d/a01bc76df178a4c91c90245c484d95ef2dfcc1.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0d/a01bc76df178a4c91c90245c484d95ef2dfcc1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_slatec.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0d/a01bc76df178a4c91c90245c484d95ef2dfcc1.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_slatec.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/14 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_masks.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/14/dde896fddfd8d0dc7216b265113be76a47cf3f.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/14/dde896fddfd8d0dc7216b265113be76a47cf3f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_masks.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/14/dde896fddfd8d0dc7216b265113be76a47cf3f.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_masks.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0d + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_slatec.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0d/a01bc76df178a4c91c90245c484d95ef2dfcc1.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0d/a01bc76df178a4c91c90245c484d95ef2dfcc1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_slatec.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0d/a01bc76df178a4c91c90245c484d95ef2dfcc1.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_slatec.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/41 + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_minpack.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/41/84449d13b44fd3e2a5697e24e6277267794cf1.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/41/84449d13b44fd3e2a5697e24e6277267794cf1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_minpack.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/41/84449d13b44fd3e2a5697e24e6277267794cf1.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_minpack.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0c objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0c/afea64204b90c9b31e433848a992ef80e887bf.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/0c/afea64204b90c9b31e433848a992ef80e887bf.debug @@ -50005,16 +50044,16 @@ chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/11/d2050414411f11f3ac0cec16150e3ca78e3147.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libdxtbxspotfinder.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/11/d2050414411f11f3ac0cec16150e3ca78e3147.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libdxtbxspotfinder.so.0.0.1 - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/97 - objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/97/6f9af382034d74bd0ee2f7e1de13cc6f67ff6e.debug - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/97/6f9af382034d74bd0ee2f7e1de13cc6f67ff6e.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 - objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/97/6f9af382034d74bd0ee2f7e1de13cc6f67ff6e.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/25 objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcbf-private.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/25/a475e4ac49f117c5cce9db51f3977d4c13dc46.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/25/a475e4ac49f117c5cce9db51f3977d4c13dc46.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcbf-private.so.0.0.1 objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/25/a475e4ac49f117c5cce9db51f3977d4c13dc46.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcbf-private.so.0.0.1 + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/97 + objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/97/6f9af382034d74bd0ee2f7e1de13cc6f67ff6e.debug + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/97/6f9af382034d74bd0ee2f7e1de13cc6f67ff6e.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 + objcopy --add-gnu-debuglink debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/97/6f9af382034d74bd0ee2f7e1de13cc6f67ff6e.debug debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/eb objcopy --only-keep-debug --compress-debug-sections debian/libcctbx0/usr/lib/aarch64-linux-gnu/libccp4io.so.0.0.1 debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/eb/58622dc1e64d09adabfb5df2c69d5a5139f084.debug chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/usr/lib/debug/.build-id/eb/58622dc1e64d09adabfb5df2c69d5a5139f084.debug @@ -50040,11 +50079,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/d3ff42990016cc6a4b38d5ea61c88b8689e496.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/d3ff42990016cc6a4b38d5ea61c88b8689e496.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/b1c2b7faa071293c701216d0b7b85a75da27d0.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/b1c2b7faa071293c701216d0b7b85a75da27d0.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/b1c2b7faa071293c701216d0b7b85a75da27d0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/588e16dfef3263de4d5f861fd39eb760be1299.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/588e16dfef3263de4d5f861fd39eb760be1299.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/588e16dfef3263de4d5f861fd39eb760be1299.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/08 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/08/052f75429e756243d4396aba0dd359d7dd0246.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/08/052f75429e756243d4396aba0dd359d7dd0246.debug @@ -50055,11 +50094,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/3d0bbf08b5dbd1bcf22e727b2cad89a4fe27db.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/3d0bbf08b5dbd1bcf22e727b2cad89a4fe27db.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/588e16dfef3263de4d5f861fd39eb760be1299.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/588e16dfef3263de4d5f861fd39eb760be1299.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/13/588e16dfef3263de4d5f861fd39eb760be1299.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/b1c2b7faa071293c701216d0b7b85a75da27d0.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/b1c2b7faa071293c701216d0b7b85a75da27d0.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/31/b1c2b7faa071293c701216d0b7b85a75da27d0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9/cf8c46ae1f94e4f1dcb08b732d1eb0efff3630.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c9/cf8c46ae1f94e4f1dcb08b732d1eb0efff3630.debug @@ -50085,6 +50124,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/4ac1e3e1bbb9bce6dbd29a276bb1f617d9a437.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/4ac1e3e1bbb9bce6dbd29a276bb1f617d9a437.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/4f8fe2afbef9e8d1206e76309efd3986e745c0.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/4f8fe2afbef9e8d1206e76309efd3986e745c0.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/4f8fe2afbef9e8d1206e76309efd3986e745c0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/40 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/40/c69357e1922e409df5931cad1ec115350b3a90.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/40/c69357e1922e409df5931cad1ec115350b3a90.debug @@ -50095,11 +50139,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/fab53812526902a3693b86e01aeb53d2f58daa.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a2/fab53812526902a3693b86e01aeb53d2f58daa.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/c299264a019f7ea6b8cbd27d879db79350b6ee.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/c299264a019f7ea6b8cbd27d879db79350b6ee.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/c299264a019f7ea6b8cbd27d879db79350b6ee.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0/5dcc72000ae497b5bb00e66f981ddf07326637.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f0/5dcc72000ae497b5bb00e66f981ddf07326637.debug @@ -50110,21 +50149,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/08283ff3853538101043106a21f81906338575.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/cf/08283ff3853538101043106a21f81906338575.debug debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/4f8fe2afbef9e8d1206e76309efd3986e745c0.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/4f8fe2afbef9e8d1206e76309efd3986e745c0.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/4f8fe2afbef9e8d1206e76309efd3986e745c0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/ee8d12395901abe7aea3222fb5e7605bc17ef0.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/ee8d12395901abe7aea3222fb5e7605bc17ef0.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/ee8d12395901abe7aea3222fb5e7605bc17ef0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/c299264a019f7ea6b8cbd27d879db79350b6ee.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/c299264a019f7ea6b8cbd27d879db79350b6ee.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/c299264a019f7ea6b8cbd27d879db79350b6ee.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/8f3e643ffc16cabfb54452b38423cd7efebf27.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/8f3e643ffc16cabfb54452b38423cd7efebf27.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/8f3e643ffc16cabfb54452b38423cd7efebf27.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/ee8d12395901abe7aea3222fb5e7605bc17ef0.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/ee8d12395901abe7aea3222fb5e7605bc17ef0.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/ee8d12395901abe7aea3222fb5e7605bc17ef0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b0 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b0/4ad8603fde263c51f52d83d51d997d2670aa9f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b0/4ad8603fde263c51f52d83d51d997d2670aa9f.debug @@ -50145,26 +50184,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/49269b8cdfef48c93cc10c3b8dbeeb3f78b21c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/49269b8cdfef48c93cc10c3b8dbeeb3f78b21c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/9986c210d19abfbbcc5ce9c7ee679dc7fde4db.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/9986c210d19abfbbcc5ce9c7ee679dc7fde4db.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/9986c210d19abfbbcc5ce9c7ee679dc7fde4db.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/55 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/55/77b228b9ef2ed6c9bf7c854e8b071aa2d22cc2.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/55/77b228b9ef2ed6c9bf7c854e8b071aa2d22cc2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/55/77b228b9ef2ed6c9bf7c854e8b071aa2d22cc2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/9986c210d19abfbbcc5ce9c7ee679dc7fde4db.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/9986c210d19abfbbcc5ce9c7ee679dc7fde4db.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5a/9986c210d19abfbbcc5ce9c7ee679dc7fde4db.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/29 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/29/04d6912f857c1e4400e4929a0e91e4378ed21c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/29/04d6912f857c1e4400e4929a0e91e4378ed21c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/29/04d6912f857c1e4400e4929a0e91e4378ed21c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/7f7cebc52bbc273339082de6623c24afe89a15.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/7f7cebc52bbc273339082de6623c24afe89a15.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/7f7cebc52bbc273339082de6623c24afe89a15.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d6 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d6/ef8afc0994d19ae46fc9e9af0b7fe39307f7a6.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d6/ef8afc0994d19ae46fc9e9af0b7fe39307f7a6.debug @@ -50175,51 +50209,61 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/cee32038753779efafba021a0173d1d4733b50.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/cee32038753779efafba021a0173d1d4733b50.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/f3d7ab72cbaf5cb3f5affc3a0c3a27d5754a8a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/f3d7ab72cbaf5cb3f5affc3a0c3a27d5754a8a.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/f3d7ab72cbaf5cb3f5affc3a0c3a27d5754a8a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/7f7cebc52bbc273339082de6623c24afe89a15.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/7f7cebc52bbc273339082de6623c24afe89a15.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4e/7f7cebc52bbc273339082de6623c24afe89a15.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/fbb9939943923ecf118bf8865e02fe8a6e98e7.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/fbb9939943923ecf118bf8865e02fe8a6e98e7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/fbb9939943923ecf118bf8865e02fe8a6e98e7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/7b856f5cc756f84b2fc2e6d951ea745f41dbd5.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/7b856f5cc756f84b2fc2e6d951ea745f41dbd5.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/7b856f5cc756f84b2fc2e6d951ea745f41dbd5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/f3d7ab72cbaf5cb3f5affc3a0c3a27d5754a8a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/f3d7ab72cbaf5cb3f5affc3a0c3a27d5754a8a.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/f3d7ab72cbaf5cb3f5affc3a0c3a27d5754a8a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/55a6801bd8a5faacf4b8826da062846cf3be2b.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/55a6801bd8a5faacf4b8826da062846cf3be2b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/55a6801bd8a5faacf4b8826da062846cf3be2b.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/7b856f5cc756f84b2fc2e6d951ea745f41dbd5.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/7b856f5cc756f84b2fc2e6d951ea745f41dbd5.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1e/7b856f5cc756f84b2fc2e6d951ea745f41dbd5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/570e367f1d60a9fbf3c6e03f76091b80005ef7.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/570e367f1d60a9fbf3c6e03f76091b80005ef7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3b/570e367f1d60a9fbf3c6e03f76091b80005ef7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9f + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9f/45773c8aa16a9895bf091c2812a68d1e052533.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9f/45773c8aa16a9895bf091c2812a68d1e052533.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9f/45773c8aa16a9895bf091c2812a68d1e052533.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/81b0ed5ac4338e62a79987db6a220a32d1732e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/81b0ed5ac4338e62a79987db6a220a32d1732e.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/81b0ed5ac4338e62a79987db6a220a32d1732e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/857a44edf46fb7c126509a234ffe37c623a7f1.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/857a44edf46fb7c126509a234ffe37c623a7f1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/857a44edf46fb7c126509a234ffe37c623a7f1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/47f14ad246273dde85fcfe7c873910e3983133.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/47f14ad246273dde85fcfe7c873910e3983133.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/47f14ad246273dde85fcfe7c873910e3983133.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/8b9797c5e9f820823857661546d816bbf63803.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/8b9797c5e9f820823857661546d816bbf63803.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/8b9797c5e9f820823857661546d816bbf63803.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/857a44edf46fb7c126509a234ffe37c623a7f1.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/857a44edf46fb7c126509a234ffe37c623a7f1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/857a44edf46fb7c126509a234ffe37c623a7f1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/6f5c3b3ec70949e818c86c953bbbc993c16534.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/6f5c3b3ec70949e818c86c953bbbc993c16534.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/6f5c3b3ec70949e818c86c953bbbc993c16534.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reduce_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/896b49c836b0231489efd0e19a1e06814e627d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/896b49c836b0231489efd0e19a1e06814e627d.debug @@ -50230,16 +50274,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab/a5c6798c2557ef7d5daf5d477971a7d55472ad.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ab/a5c6798c2557ef7d5daf5d477971a7d55472ad.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9f - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9f/45773c8aa16a9895bf091c2812a68d1e052533.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9f/45773c8aa16a9895bf091c2812a68d1e052533.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9f/45773c8aa16a9895bf091c2812a68d1e052533.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/6f5c3b3ec70949e818c86c953bbbc993c16534.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/6f5c3b3ec70949e818c86c953bbbc993c16534.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a3/6f5c3b3ec70949e818c86c953bbbc993c16534.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/8b9797c5e9f820823857661546d816bbf63803.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/8b9797c5e9f820823857661546d816bbf63803.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b9/8b9797c5e9f820823857661546d816bbf63803.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/e9a282e8d50b3e35ed9e62ae00c9d84f8ff0e5.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d2/e9a282e8d50b3e35ed9e62ae00c9d84f8ff0e5.debug @@ -50250,16 +50289,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56/487cc5c73b2a7310add6d465aef3e8e874ddd0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56/487cc5c73b2a7310add6d465aef3e8e874ddd0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b/d6bf0ddad1cf9ab4ba5e356e8ce312daf15b12.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b/d6bf0ddad1cf9ab4ba5e356e8ce312daf15b12.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b/d6bf0ddad1cf9ab4ba5e356e8ce312daf15b12.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/90 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/90/46abe154ca73054c61a41ffd64171a5ef7ab41.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/90/46abe154ca73054c61a41ffd64171a5ef7ab41.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/90/46abe154ca73054c61a41ffd64171a5ef7ab41.debug debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/88 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/88/2215a3be7c6b35f468612a615a432aa189342a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/88/2215a3be7c6b35f468612a615a432aa189342a.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/88/2215a3be7c6b35f468612a615a432aa189342a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b/d6bf0ddad1cf9ab4ba5e356e8ce312daf15b12.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b/d6bf0ddad1cf9ab4ba5e356e8ce312daf15b12.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8b/d6bf0ddad1cf9ab4ba5e356e8ce312daf15b12.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/67 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/67/e09bd535c460735aa5a52663e4e88faf8a1ee0.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/67/e09bd535c460735aa5a52663e4e88faf8a1ee0.debug @@ -50270,11 +50314,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22/bb91a91be241821f3f5147a53c039505acd59c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/22/bb91a91be241821f3f5147a53c039505acd59c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/88 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/88/2215a3be7c6b35f468612a615a432aa189342a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/88/2215a3be7c6b35f468612a615a432aa189342a.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/88/2215a3be7c6b35f468612a615a432aa189342a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6f objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6f/49a6444600b095ab20b5327da1b4a3411f3a5c.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6f/49a6444600b095ab20b5327da1b4a3411f3a5c.debug @@ -50300,6 +50339,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/81325f81eb64b676918112c6f73a2c2e4563c2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bb/81325f81eb64b676918112c6f73a2c2e4563c2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/b82d871c685ea59b091118b12aa720a76d0ed2.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/b82d871c685ea59b091118b12aa720a76d0ed2.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/b82d871c685ea59b091118b12aa720a76d0ed2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9/2b42b58c0e780a5fadf7593ccf522851ef6821.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9/2b42b58c0e780a5fadf7593ccf522851ef6821.debug @@ -50316,45 +50360,40 @@ strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/93108c52cba29ba31db84c41df656e5125f3f0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/b82d871c685ea59b091118b12aa720a76d0ed2.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/b82d871c685ea59b091118b12aa720a76d0ed2.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/b82d871c685ea59b091118b12aa720a76d0ed2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/14bc4cbd68efb3193e7e47203005f5d4157026.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/14bc4cbd68efb3193e7e47203005f5d4157026.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/14bc4cbd68efb3193e7e47203005f5d4157026.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/e4507a4a7ca90c5d115423ba76050dd1446366.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/e4507a4a7ca90c5d115423ba76050dd1446366.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/e4507a4a7ca90c5d115423ba76050dd1446366.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/24741dc64342b81d181877ece4b59a1f06f8c6.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/24741dc64342b81d181877ece4b59a1f06f8c6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/24741dc64342b81d181877ece4b59a1f06f8c6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/e4507a4a7ca90c5d115423ba76050dd1446366.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/e4507a4a7ca90c5d115423ba76050dd1446366.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/71/e4507a4a7ca90c5d115423ba76050dd1446366.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/37e86be7a3fc967cbb96979edc2caae21328e9.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/37e86be7a3fc967cbb96979edc2caae21328e9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fb/37e86be7a3fc967cbb96979edc2caae21328e9.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/2f3d3a728b142aaafd39ffa67f1d96403d0bdb.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/2f3d3a728b142aaafd39ffa67f1d96403d0bdb.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/2f3d3a728b142aaafd39ffa67f1d96403d0bdb.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/e926a52700ab297cfd032870c524d58125c999.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/e926a52700ab297cfd032870c524d58125c999.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/e926a52700ab297cfd032870c524d58125c999.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9/3febbac6369db30af31342ef752131d1b06734.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9/3febbac6369db30af31342ef752131d1b06734.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9/3febbac6369db30af31342ef752131d1b06734.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/2f3d3a728b142aaafd39ffa67f1d96403d0bdb.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/2f3d3a728b142aaafd39ffa67f1d96403d0bdb.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8c/2f3d3a728b142aaafd39ffa67f1d96403d0bdb.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/05 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/05/e05a3b5c4801822e037923c3bab5d8db64e7c7.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/05/e05a3b5c4801822e037923c3bab5d8db64e7c7.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/05/e05a3b5c4801822e037923c3bab5d8db64e7c7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4/d1a3114f6c0c4c73da4ffc7662ee338b13fa72.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4/d1a3114f6c0c4c73da4ffc7662ee338b13fa72.debug @@ -50365,31 +50404,31 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/3f23adfcd0c41e7751b3991bf572d103ec0a86.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/49/3f23adfcd0c41e7751b3991bf572d103ec0a86.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/05 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/05/e05a3b5c4801822e037923c3bab5d8db64e7c7.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/05/e05a3b5c4801822e037923c3bab5d8db64e7c7.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/05/e05a3b5c4801822e037923c3bab5d8db64e7c7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/046bb31784f76441a4a69db76dcd3aba40047f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/046bb31784f76441a4a69db76dcd3aba40047f.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/046bb31784f76441a4a69db76dcd3aba40047f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/e926a52700ab297cfd032870c524d58125c999.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/e926a52700ab297cfd032870c524d58125c999.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/e926a52700ab297cfd032870c524d58125c999.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/46a3dbc66d8e2d149acd67401a147c7639c0dc.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/46a3dbc66d8e2d149acd67401a147c7639c0dc.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/46a3dbc66d8e2d149acd67401a147c7639c0dc.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/d01cd890c75e7f8a08433470836ecd4e61d515.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/d01cd890c75e7f8a08433470836ecd4e61d515.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/d01cd890c75e7f8a08433470836ecd4e61d515.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/046bb31784f76441a4a69db76dcd3aba40047f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/046bb31784f76441a4a69db76dcd3aba40047f.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3a/046bb31784f76441a4a69db76dcd3aba40047f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e6/8cc90577542fbbfc1c84146b5d4d652c8b4ff2.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e6/8cc90577542fbbfc1c84146b5d4d652c8b4ff2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e6/8cc90577542fbbfc1c84146b5d4d652c8b4ff2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/d01cd890c75e7f8a08433470836ecd4e61d515.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/d01cd890c75e7f8a08433470836ecd4e61d515.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fc/d01cd890c75e7f8a08433470836ecd4e61d515.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79/f728f432b1beb28ed4feba0d980fcfc14e704e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/79/f728f432b1beb28ed4feba0d980fcfc14e704e.debug @@ -50400,16 +50439,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/2b63799a2a5f2810070ba75b9abf64bf1336f6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/10/2b63799a2a5f2810070ba75b9abf64bf1336f6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/322cabb30799a9ea61e6169bf30c097784f520.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/322cabb30799a9ea61e6169bf30c097784f520.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/322cabb30799a9ea61e6169bf30c097784f520.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/af4222d3f6787bf715bf5aad9f650db05f838a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/af4222d3f6787bf715bf5aad9f650db05f838a.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/af4222d3f6787bf715bf5aad9f650db05f838a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/4aa7cb0ddab8bc7b0e712bbcc4f1404df653bd.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/4aa7cb0ddab8bc7b0e712bbcc4f1404df653bd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/e7/4aa7cb0ddab8bc7b0e712bbcc4f1404df653bd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/322cabb30799a9ea61e6169bf30c097784f520.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/322cabb30799a9ea61e6169bf30c097784f520.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/322cabb30799a9ea61e6169bf30c097784f520.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bd/137e107859d1699926647365f3068aaa26f77a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bd/137e107859d1699926647365f3068aaa26f77a.debug @@ -50420,31 +50464,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/8067b253ad65646bd0f4aeb63dfc3a35f9ca41.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/8067b253ad65646bd0f4aeb63dfc3a35f9ca41.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/5caa78f964c957b3885bded033e6247c4cf054.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/5caa78f964c957b3885bded033e6247c4cf054.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/5caa78f964c957b3885bded033e6247c4cf054.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/40e48480126af60bb155d07810e02172dcb645.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/40e48480126af60bb155d07810e02172dcb645.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/40e48480126af60bb155d07810e02172dcb645.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/a22288bd091fa3336a66dc873e8a8fd732239f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/a22288bd091fa3336a66dc873e8a8fd732239f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/db/a22288bd091fa3336a66dc873e8a8fd732239f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/af4222d3f6787bf715bf5aad9f650db05f838a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/af4222d3f6787bf715bf5aad9f650db05f838a.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/af4222d3f6787bf715bf5aad9f650db05f838a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/11e0bf888a20ceb963f9b0dd1a42a1ce841ba4.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/11e0bf888a20ceb963f9b0dd1a42a1ce841ba4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0d/11e0bf888a20ceb963f9b0dd1a42a1ce841ba4.debug debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/40e48480126af60bb155d07810e02172dcb645.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/40e48480126af60bb155d07810e02172dcb645.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/30/40e48480126af60bb155d07810e02172dcb645.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/40 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/40/27d192ee3cd5c97d2e0ac4f112d7541e7de020.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/40/27d192ee3cd5c97d2e0ac4f112d7541e7de020.debug @@ -50455,21 +50489,26 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/66/c6b6413ba157bfa5cab4cbea9fffa26e2d481f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/66/c6b6413ba157bfa5cab4cbea9fffa26e2d481f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/78b649c3dd2b7b491fcffc3391f9efb77cff54.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/78b649c3dd2b7b491fcffc3391f9efb77cff54.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/78b649c3dd2b7b491fcffc3391f9efb77cff54.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/2114e4e733ec33f4752e619c8194a4d1ea6684.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/2114e4e733ec33f4752e619c8194a4d1ea6684.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/2114e4e733ec33f4752e619c8194a4d1ea6684.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/6d9719e6166a30ded1c3eef99f58fe875f2c6f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/6d9719e6166a30ded1c3eef99f58fe875f2c6f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/72/6d9719e6166a30ded1c3eef99f58fe875f2c6f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/2114e4e733ec33f4752e619c8194a4d1ea6684.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/2114e4e733ec33f4752e619c8194a4d1ea6684.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/12/2114e4e733ec33f4752e619c8194a4d1ea6684.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/78b649c3dd2b7b491fcffc3391f9efb77cff54.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/78b649c3dd2b7b491fcffc3391f9efb77cff54.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/37/78b649c3dd2b7b491fcffc3391f9efb77cff54.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/5caa78f964c957b3885bded033e6247c4cf054.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/5caa78f964c957b3885bded033e6247c4cf054.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7e/5caa78f964c957b3885bded033e6247c4cf054.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/86 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/86/c3b9709b79eb92f8fe52c68cb33003cba1ce25.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/86/c3b9709b79eb92f8fe52c68cb33003cba1ce25.debug @@ -50495,11 +50534,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/b70b45662c2a68ca46ef3494df279fcaa8d359.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b1/b70b45662c2a68ca46ef3494df279fcaa8d359.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/376b9c7b16cc70947132fab75dd95cbe15bf4f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/376b9c7b16cc70947132fab75dd95cbe15bf4f.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/376b9c7b16cc70947132fab75dd95cbe15bf4f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/024ca0c77ae2cbc971376801f2d3488ba9ea41.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/16/024ca0c77ae2cbc971376801f2d3488ba9ea41.debug @@ -50510,6 +50544,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b/7a820f4997d53aa1abfe97f4aaae0315833c42.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/6b/7a820f4997d53aa1abfe97f4aaae0315833c42.debug debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/7b502b74b8c59561fb11e696fe4d39467b73c7.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/7b502b74b8c59561fb11e696fe4d39467b73c7.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/7b502b74b8c59561fb11e696fe4d39467b73c7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/09 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/09/9e830caebcfd078bea058ab2f210e055b84572.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/09/9e830caebcfd078bea058ab2f210e055b84572.debug @@ -50520,11 +50559,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b2/2b69c3b2393a1396a865dff7c58264b67070cf.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b2/2b69c3b2393a1396a865dff7c58264b67070cf.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/7b502b74b8c59561fb11e696fe4d39467b73c7.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/7b502b74b8c59561fb11e696fe4d39467b73c7.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/15/7b502b74b8c59561fb11e696fe4d39467b73c7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/90 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/90/07262c541b204f48af437c4d26a61511330f21.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/90/07262c541b204f48af437c4d26a61511330f21.debug @@ -50535,6 +50569,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/3e9e171211d794d86ea16ee5db07d34df94058.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/3e9e171211d794d86ea16ee5db07d34df94058.debug debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/df + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/df/0b653796eb93bf3dbcc51c5cc4c3ae2c21f474.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/df/0b653796eb93bf3dbcc51c5cc4c3ae2c21f474.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/df/0b653796eb93bf3dbcc51c5cc4c3ae2c21f474.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/a82d042cc413ea2da247744a3a942e0ef66409.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/a82d042cc413ea2da247744a3a942e0ef66409.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/a82d042cc413ea2da247744a3a942e0ef66409.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/78611e9f1550e14047353d6c0f4c6b90362cec.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c3/78611e9f1550e14047353d6c0f4c6b90362cec.debug @@ -50545,71 +50589,61 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4a/7241b8c80b07cada8b1c7b224433f57851e88c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4a/7241b8c80b07cada8b1c7b224433f57851e88c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/376b9c7b16cc70947132fab75dd95cbe15bf4f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/376b9c7b16cc70947132fab75dd95cbe15bf4f.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/376b9c7b16cc70947132fab75dd95cbe15bf4f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ef objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ef/9cc0bc8c9493fcb6eed2e7071b07f65693a139.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ef/9cc0bc8c9493fcb6eed2e7071b07f65693a139.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ef/9cc0bc8c9493fcb6eed2e7071b07f65693a139.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/a82d042cc413ea2da247744a3a942e0ef66409.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/a82d042cc413ea2da247744a3a942e0ef66409.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/af/a82d042cc413ea2da247744a3a942e0ef66409.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/df - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/df/0b653796eb93bf3dbcc51c5cc4c3ae2c21f474.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/df/0b653796eb93bf3dbcc51c5cc4c3ae2c21f474.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/df/0b653796eb93bf3dbcc51c5cc4c3ae2c21f474.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/31e5aa599fe712e4775680bf5d099c9efab69d.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/31e5aa599fe712e4775680bf5d099c9efab69d.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/31e5aa599fe712e4775680bf5d099c9efab69d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/a870c133e0ed3929afe631b989d53b97f09565.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/a870c133e0ed3929afe631b989d53b97f09565.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/36/a870c133e0ed3929afe631b989d53b97f09565.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/31e5aa599fe712e4775680bf5d099c9efab69d.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/31e5aa599fe712e4775680bf5d099c9efab69d.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/31e5aa599fe712e4775680bf5d099c9efab69d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ef objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ef/57db0f3c8887e228a9f903abf3a7cb5b19a2e7.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ef/57db0f3c8887e228a9f903abf3a7cb5b19a2e7.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ef/57db0f3c8887e228a9f903abf3a7cb5b19a2e7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/e4e2d02ca30cf20bcc6febada82a5330bb03d7.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/e4e2d02ca30cf20bcc6febada82a5330bb03d7.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/e4e2d02ca30cf20bcc6febada82a5330bb03d7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a8 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a8/fd90b450c218747834ae7ff94715dd4c8fa022.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a8/fd90b450c218747834ae7ff94715dd4c8fa022.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a8/fd90b450c218747834ae7ff94715dd4c8fa022.debug debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/87b7e84b522f48970ac7eb288750a9c145d8de.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/87b7e84b522f48970ac7eb288750a9c145d8de.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/87b7e84b522f48970ac7eb288750a9c145d8de.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/482727fb4c67f1f0f71bce0508a66dda3ed0dd.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/482727fb4c67f1f0f71bce0508a66dda3ed0dd.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/482727fb4c67f1f0f71bce0508a66dda3ed0dd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/b9a9cca1bacc6551ae837d9115fbf1bfbf4f7a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/b9a9cca1bacc6551ae837d9115fbf1bfbf4f7a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/fe/b9a9cca1bacc6551ae837d9115fbf1bfbf4f7a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/482727fb4c67f1f0f71bce0508a66dda3ed0dd.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/482727fb4c67f1f0f71bce0508a66dda3ed0dd.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2d/482727fb4c67f1f0f71bce0508a66dda3ed0dd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/0cffb6907d0a8531ba8d8bcadfe0af9ddc4391.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/0cffb6907d0a8531ba8d8bcadfe0af9ddc4391.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/26/0cffb6907d0a8531ba8d8bcadfe0af9ddc4391.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/e4e2d02ca30cf20bcc6febada82a5330bb03d7.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/e4e2d02ca30cf20bcc6febada82a5330bb03d7.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/54/e4e2d02ca30cf20bcc6febada82a5330bb03d7.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/60 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/60/bcf999266cdea627212e502073a3ae5e3f0b4f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/60/bcf999266cdea627212e502073a3ae5e3f0b4f.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/60/bcf999266cdea627212e502073a3ae5e3f0b4f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/87b7e84b522f48970ac7eb288750a9c145d8de.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/87b7e84b522f48970ac7eb288750a9c145d8de.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b5/87b7e84b522f48970ac7eb288750a9c145d8de.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/00ddb438db4c03ac9306284ec78466b0916b5a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/00ddb438db4c03ac9306284ec78466b0916b5a.debug @@ -50625,16 +50659,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/87/a62fe0cff34f019cafbc8f638103b7a3f46a1d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/87/a62fe0cff34f019cafbc8f638103b7a3f46a1d.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/586bd0b9f6b0923d9ad7408144e000e2fad8e8.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/586bd0b9f6b0923d9ad7408144e000e2fad8e8.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/586bd0b9f6b0923d9ad7408144e000e2fad8e8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/00 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/00/f6db8b143b8ba346bb1077a68cde00dbf970f5.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/00/f6db8b143b8ba346bb1077a68cde00dbf970f5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/00/f6db8b143b8ba346bb1077a68cde00dbf970f5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/586bd0b9f6b0923d9ad7408144e000e2fad8e8.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/586bd0b9f6b0923d9ad7408144e000e2fad8e8.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ba/586bd0b9f6b0923d9ad7408144e000e2fad8e8.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/60 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/60/bcf999266cdea627212e502073a3ae5e3f0b4f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/60/bcf999266cdea627212e502073a3ae5e3f0b4f.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/60/bcf999266cdea627212e502073a3ae5e3f0b4f.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/85 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/85/2d4ac4f6a2bd7f1a7a066cc239eff6838bf7b9.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/85/2d4ac4f6a2bd7f1a7a066cc239eff6838bf7b9.debug @@ -50645,11 +50684,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/84b06d6381e4f0156bf4b757e511b57de67dca.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ad/84b06d6381e4f0156bf4b757e511b57de67dca.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04/13f9464e952f3a7f34c323346769d62608b7be.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04/13f9464e952f3a7f34c323346769d62608b7be.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04/13f9464e952f3a7f34c323346769d62608b7be.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/8406c5778b557f4e60fa19ce00867fbff3f743.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/96/8406c5778b557f4e60fa19ce00867fbff3f743.debug @@ -50660,6 +50694,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9a/a5a0ad41ae20dd89a62af11d92177a643d64dd.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9a/a5a0ad41ae20dd89a62af11d92177a643d64dd.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04/13f9464e952f3a7f34c323346769d62608b7be.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04/13f9464e952f3a7f34c323346769d62608b7be.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04/13f9464e952f3a7f34c323346769d62608b7be.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a4 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a4/89ad3b484b0ddb2f93c870163a403c8157dd2e.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a4/89ad3b484b0ddb2f93c870163a403c8157dd2e.debug @@ -50670,16 +50709,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ed/a712ae1bc61aa6b5bbe76cca7c463970c2181c.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ed/a712ae1bc61aa6b5bbe76cca7c463970c2181c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/7945fe11536c55f81a2b6d1883d1a743a79f7e.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/7945fe11536c55f81a2b6d1883d1a743a79f7e.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/7945fe11536c55f81a2b6d1883d1a743a79f7e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/c94d1a1ea10bfa27403a6955f184f8715ced72.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/c94d1a1ea10bfa27403a6955f184f8715ced72.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1f/c94d1a1ea10bfa27403a6955f184f8715ced72.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d/4b57eab947dff32acbea295100f878ef05a625.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d/4b57eab947dff32acbea295100f878ef05a625.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d/4b57eab947dff32acbea295100f878ef05a625.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/7945fe11536c55f81a2b6d1883d1a743a79f7e.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/7945fe11536c55f81a2b6d1883d1a743a79f7e.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/76/7945fe11536c55f81a2b6d1883d1a743a79f7e.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f4 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f4/8fd577c6db45cec3beeb1e577c3f04b49bc85f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f4/8fd577c6db45cec3beeb1e577c3f04b49bc85f.debug @@ -50690,11 +50734,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac/a71d8f69b7729f7db1180d5b940fb51299e387.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ac/a71d8f69b7729f7db1180d5b940fb51299e387.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d/4b57eab947dff32acbea295100f878ef05a625.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d/4b57eab947dff32acbea295100f878ef05a625.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3d/4b57eab947dff32acbea295100f878ef05a625.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/e03faf3cc16ed90dcfc5fa1062fe70a7b9e460.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f5/e03faf3cc16ed90dcfc5fa1062fe70a7b9e460.debug @@ -50705,31 +50744,26 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/75/f9193c5ed0c4b6f938c4cfae9c2affcd8711f0.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/75/f9193c5ed0c4b6f938c4cfae9c2affcd8711f0.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/cf05ef09986b8686ae745447715422c5105f71.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/cf05ef09986b8686ae745447715422c5105f71.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/cf05ef09986b8686ae745447715422c5105f71.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/1e8346b8d27068bfb55f6181fb35cf66df51ef.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/1e8346b8d27068bfb55f6181fb35cf66df51ef.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/82/1e8346b8d27068bfb55f6181fb35cf66df51ef.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/8ed2db41b81199a4cdb31dc986b668130583d1.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/8ed2db41b81199a4cdb31dc986b668130583d1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/8ed2db41b81199a4cdb31dc986b668130583d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1b objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1b/1dbfe5f5f2b884e016bd882534ad854e0936de.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1b/1dbfe5f5f2b884e016bd882534ad854e0936de.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1b/1dbfe5f5f2b884e016bd882534ad854e0936de.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d0 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d0/53f36d0d32e4c9c35421aae176cae2306d0e80.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d0/53f36d0d32e4c9c35421aae176cae2306d0e80.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d0/53f36d0d32e4c9c35421aae176cae2306d0e80.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/cf05ef09986b8686ae745447715422c5105f71.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/cf05ef09986b8686ae745447715422c5105f71.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/cf05ef09986b8686ae745447715422c5105f71.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/8ed2db41b81199a4cdb31dc986b668130583d1.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/8ed2db41b81199a4cdb31dc986b668130583d1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/51/8ed2db41b81199a4cdb31dc986b668130583d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/3a1f5636fb89a795896e0afb293a3a62b03a92.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/3a1f5636fb89a795896e0afb293a3a62b03a92.debug @@ -50740,6 +50774,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68/18af3bcc9ec1140533a1816194d41e82eb6bc6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/68/18af3bcc9ec1140533a1816194d41e82eb6bc6.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d0 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d0/53f36d0d32e4c9c35421aae176cae2306d0e80.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d0/53f36d0d32e4c9c35421aae176cae2306d0e80.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d0/53f36d0d32e4c9c35421aae176cae2306d0e80.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/04962c47d66facd14714a4c3e7e3d481317b46.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/04962c47d66facd14714a4c3e7e3d481317b46.debug @@ -50750,111 +50789,106 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/9d2a4facf3c50ddff9e34aa8b67c535f985db5.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a0/9d2a4facf3c50ddff9e34aa8b67c535f985db5.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/e85d95dfbc0952bb8f3744a91db78808415039.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/e85d95dfbc0952bb8f3744a91db78808415039.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/e85d95dfbc0952bb8f3744a91db78808415039.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/9275b069d651fc2ad3a6d717020d386548c64a.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/9275b069d651fc2ad3a6d717020d386548c64a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/9275b069d651fc2ad3a6d717020d386548c64a.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/826d17f0e1c6f0a71087b6b8f4b587a8a3fb62.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/826d17f0e1c6f0a71087b6b8f4b587a8a3fb62.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/826d17f0e1c6f0a71087b6b8f4b587a8a3fb62.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56/69d605d1539104416627aa0f0dd3fa35279300.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56/69d605d1539104416627aa0f0dd3fa35279300.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56/69d605d1539104416627aa0f0dd3fa35279300.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/826d17f0e1c6f0a71087b6b8f4b587a8a3fb62.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/826d17f0e1c6f0a71087b6b8f4b587a8a3fb62.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/826d17f0e1c6f0a71087b6b8f4b587a8a3fb62.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c/a034ed73cbccffda9b3bd607679f51eec07c91.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c/a034ed73cbccffda9b3bd607679f51eec07c91.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/3c/a034ed73cbccffda9b3bd607679f51eec07c91.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1c - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1c/079dec16b18813b411b32af0936fe5cb0d6c28.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1c/079dec16b18813b411b32af0936fe5cb0d6c28.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1c/079dec16b18813b411b32af0936fe5cb0d6c28.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c8 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c8/f5a48607c31b7b1695c9bda30950304a81096c.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c8/f5a48607c31b7b1695c9bda30950304a81096c.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c8/f5a48607c31b7b1695c9bda30950304a81096c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/e85d95dfbc0952bb8f3744a91db78808415039.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/e85d95dfbc0952bb8f3744a91db78808415039.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/99/e85d95dfbc0952bb8f3744a91db78808415039.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/17 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/17/17a6767994a96d771baa7ec376b728f001e9f4.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/17/17a6767994a96d771baa7ec376b728f001e9f4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/17/17a6767994a96d771baa7ec376b728f001e9f4.debug debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1c + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1c/079dec16b18813b411b32af0936fe5cb0d6c28.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1c/079dec16b18813b411b32af0936fe5cb0d6c28.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/1c/079dec16b18813b411b32af0936fe5cb0d6c28.debug debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/d86924211d9a54fc8618739996ed36751401d9.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/d86924211d9a54fc8618739996ed36751401d9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/d86924211d9a54fc8618739996ed36751401d9.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/62999ef0767e0474f72bcd7b866b8c9d8b97d1.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/62999ef0767e0474f72bcd7b866b8c9d8b97d1.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/62999ef0767e0474f72bcd7b866b8c9d8b97d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/9b85221b3ca440c152ea275fab70522094b396.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/9b85221b3ca440c152ea275fab70522094b396.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink 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debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d4/5b06ed4f9a539b204c7873781fa3e3d11b5160.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/32 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/32/aa6fd72b7b21f5674f4ff8b84faade08a25866.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/32/aa6fd72b7b21f5674f4ff8b84faade08a25866.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/32/aa6fd72b7b21f5674f4ff8b84faade08a25866.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/50b809b36392cce497325c2c1c139e313a4668.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b7/50b809b36392cce497325c2c1c139e313a4668.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink 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debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2b/c001bca30b7fa380262a92924087fa3b01a842.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/32 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/32/aa6fd72b7b21f5674f4ff8b84faade08a25866.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/32/aa6fd72b7b21f5674f4ff8b84faade08a25866.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink 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debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/c8/f5a48607c31b7b1695c9bda30950304a81096c.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/9b85221b3ca440c152ea275fab70522094b396.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/9b85221b3ca440c152ea275fab70522094b396.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/dd/9b85221b3ca440c152ea275fab70522094b396.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/62999ef0767e0474f72bcd7b866b8c9d8b97d1.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/62999ef0767e0474f72bcd7b866b8c9d8b97d1.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/62999ef0767e0474f72bcd7b866b8c9d8b97d1.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/26a3b78782e8f5f82d1c4544b2a7a6c45bb4ed.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/26a3b78782e8f5f82d1c4544b2a7a6c45bb4ed.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/27/26a3b78782e8f5f82d1c4544b2a7a6c45bb4ed.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/952fcbd0d8e0cb50fb0adefd729709ff0b7bc2.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/952fcbd0d8e0cb50fb0adefd729709ff0b7bc2.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/952fcbd0d8e0cb50fb0adefd729709ff0b7bc2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/6825da69c1ef24c308b61601ced5007a86b492.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/6825da69c1ef24c308b61601ced5007a86b492.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/45/6825da69c1ef24c308b61601ced5007a86b492.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-313-aarch64-linux-gnu.so + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/952fcbd0d8e0cb50fb0adefd729709ff0b7bc2.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/952fcbd0d8e0cb50fb0adefd729709ff0b7bc2.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/02/952fcbd0d8e0cb50fb0adefd729709ff0b7bc2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/21b76ba6651276c81ce73e42002b271ee094a2.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/21b76ba6651276c81ce73e42002b271ee094a2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/2a/21b76ba6651276c81ce73e42002b271ee094a2.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/c498d7abcdfce3dbdd5a5e437028961ab6c628.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/c498d7abcdfce3dbdd5a5e437028961ab6c628.debug - strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/c498d7abcdfce3dbdd5a5e437028961ab6c628.debug debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bd objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bd/0414b4cb0ecf7cc9def6fd895ca482868298e1.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/bd/0414b4cb0ecf7cc9def6fd895ca482868298e1.debug @@ -50865,16 +50899,21 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/4b541d0c9edd1dd9d0c69afded9aa879abd3fa.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-313-aarch64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/48/4b541d0c9edd1dd9d0c69afded9aa879abd3fa.debug debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-313-aarch64-linux-gnu.so - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/a5d6640b2cf2b535d3c8869ac4c0cdac353c4f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/a5d6640b2cf2b535d3c8869ac4c0cdac353c4f.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/a5d6640b2cf2b535d3c8869ac4c0cdac353c4f.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/c498d7abcdfce3dbdd5a5e437028961ab6c628.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/c498d7abcdfce3dbdd5a5e437028961ab6c628.debug + strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/35/c498d7abcdfce3dbdd5a5e437028961ab6c628.debug debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/c69a5ce2675eb9d1b4daf3119fd6d6a4b9fa5d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/c69a5ce2675eb9d1b4daf3119fd6d6a4b9fa5d.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7b/c69a5ce2675eb9d1b4daf3119fd6d6a4b9fa5d.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/a5d6640b2cf2b535d3c8869ac4c0cdac353c4f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/a5d6640b2cf2b535d3c8869ac4c0cdac353c4f.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/ca/a5d6640b2cf2b535d3c8869ac4c0cdac353c4f.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/96ac757f3ceeae6d0e622768fd1b9bbc63f96f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b8/96ac757f3ceeae6d0e622768fd1b9bbc63f96f.debug @@ -50885,16 +50924,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04/ec33ab729bc078144b77840a820e48c822d33a.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/04/ec33ab729bc078144b77840a820e48c822d33a.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256 - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/a8d59322c7a8871ceeedf104ad7fe48d946e1c.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/a8d59322c7a8871ceeedf104ad7fe48d946e1c.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/a8d59322c7a8871ceeedf104ad7fe48d946e1c.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/4b3be363cfc0c735d008a8c04a582856155348.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/4b3be363cfc0c735d008a8c04a582856155348.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/58/4b3be363cfc0c735d008a8c04a582856155348.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/a8d59322c7a8871ceeedf104ad7fe48d946e1c.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/a8d59322c7a8871ceeedf104ad7fe48d946e1c.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/7d/a8d59322c7a8871ceeedf104ad7fe48d946e1c.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/46 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/46/3fd86805fb63d91e644579d0e5f9e8e787880f.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/46/3fd86805fb63d91e644579d0e5f9e8e787880f.debug @@ -50925,26 +50964,36 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/18b06ab4a1caaa4f57e3e57bd84171ca598acd.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/65/18b06ab4a1caaa4f57e3e57bd84171ca598acd.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4 - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/beb1a9ae934b1fd71b5ead8c205f043c63d9af.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/beb1a9ae934b1fd71b5ead8c205f043c63d9af.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3 - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/beb1a9ae934b1fd71b5ead8c205f043c63d9af.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3 - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/ce1143bc28076d81f434d59368d3b3f9a40c1a.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/ce1143bc28076d81f434d59368d3b3f9a40c1a.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3 - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/ce1143bc28076d81f434d59368d3b3f9a40c1a.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/d8f9bcd3b82c90ea19e02b23347164d3d26a9d.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/d8f9bcd3b82c90ea19e02b23347164d3d26a9d.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8f/d8f9bcd3b82c90ea19e02b23347164d3d26a9d.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/ce1143bc28076d81f434d59368d3b3f9a40c1a.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/ce1143bc28076d81f434d59368d3b3f9a40c1a.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3 + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/ce1143bc28076d81f434d59368d3b3f9a40c1a.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3 + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/beb1a9ae934b1fd71b5ead8c205f043c63d9af.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/beb1a9ae934b1fd71b5ead8c205f043c63d9af.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3 + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/4d/beb1a9ae934b1fd71b5ead8c205f043c63d9af.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4/e6e5a57c737f6e2261d798c31834bbd70f3fd8.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4/e6e5a57c737f6e2261d798c31834bbd70f3fd8.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/b4/e6e5a57c737f6e2261d798c31834bbd70f3fd8.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/98 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/98/84fdfd29dafd6360037645a8134bf518666f7c.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/98/84fdfd29dafd6360037645a8134bf518666f7c.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3 + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/98/84fdfd29dafd6360037645a8134bf518666f7c.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3 + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a5 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a5/310545b4fa9225f43f79c477988c23d0572eb6.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a5/310545b4fa9225f43f79c477988c23d0572eb6.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3 + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a5/310545b4fa9225f43f79c477988c23d0572eb6.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9/c7d3fbdf0a66e0da75e51543e94ba9849b6040.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f9/c7d3fbdf0a66e0da75e51543e94ba9849b6040.debug @@ -50955,16 +51004,16 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/4addc8a0bc6f127d80a445d37a47e86781bffe.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/8d/4addc8a0bc6f127d80a445d37a47e86781bffe.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/98 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/98/84fdfd29dafd6360037645a8134bf518666f7c.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/98/84fdfd29dafd6360037645a8134bf518666f7c.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3 - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/98/84fdfd29dafd6360037645a8134bf518666f7c.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/69 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/69/2f6177f061d498a0238b7a688f51a73c75dd34.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/69/2f6177f061d498a0238b7a688f51a73c75dd34.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5 objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/69/2f6177f061d498a0238b7a688f51a73c75dd34.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5 + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/e9267355a0c000b1562cb16c3d39d8acff609f.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/e9267355a0c000b1562cb16c3d39d8acff609f.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2 + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/e9267355a0c000b1562cb16c3d39d8acff609f.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56/53a1e6ee19f15602cbb99f35a77970b10a13f7.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/56/53a1e6ee19f15602cbb99f35a77970b10a13f7.debug @@ -50975,16 +51024,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/161c1109d1021ff37c041385364d74f7003c2d.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9d/161c1109d1021ff37c041385364d74f7003c2d.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a5 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a5/310545b4fa9225f43f79c477988c23d0572eb6.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a5/310545b4fa9225f43f79c477988c23d0572eb6.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3 - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/a5/310545b4fa9225f43f79c477988c23d0572eb6.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3 - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2 debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/e9267355a0c000b1562cb16c3d39d8acff609f.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/e9267355a0c000b1562cb16c3d39d8acff609f.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2 - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/91/e9267355a0c000b1562cb16c3d39d8acff609f.debug debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2 install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/448d58ce97a1eaf869362b11a329ae86ee9fa1.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/5d/448d58ce97a1eaf869362b11a329ae86ee9fa1.debug @@ -51015,6 +51054,11 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f1/b8c0766fdf878b21dbd2d7469c700332680282.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/f1/b8c0766fdf878b21dbd2d7469c700332680282.debug debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry + install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5 + objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/196250486a5921b6f55a179588e4e02111ccb4.debug + chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/196250486a5921b6f55a179588e4e02111ccb4.debug + strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups + objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/196250486a5921b6f55a179588e4e02111ccb4.debug debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9e objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.getting_started debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9e/c3a753a4ffbf996fd22f7b15eda2e7d2f3f7ea.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/9e/c3a753a4ffbf996fd22f7b15eda2e7d2f3f7ea.debug @@ -51025,11 +51069,6 @@ chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0a/d154b81cda01c07bb53ee871353d1ff94018a6.debug strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/0a/d154b81cda01c07bb53ee871353d1ff94018a6.debug debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib - install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5 - objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/196250486a5921b6f55a179588e4e02111ccb4.debug - chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/196250486a5921b6f55a179588e4e02111ccb4.debug - strip --remove-section=.comment --remove-section=.note debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups - objcopy --add-gnu-debuglink debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/d5/196250486a5921b6f55a179588e4e02111ccb4.debug debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57 objcopy --only-keep-debug --compress-debug-sections debian/python3-cctbx/usr/bin/cbflib.tst_memory debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/ae128afb5c5d54a0450ba7fd2e0ed55b9c6741.debug chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/usr/lib/debug/.build-id/57/ae128afb5c5d54a0450ba7fd2e0ed55b9c6741.debug @@ -51070,362 +51109,362 @@ rm -f debian/python3-cctbx/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=pybuild install -m0755 -d debian/libcctbx0/DEBIAN - dpkg-shlibdeps -Tdebian/libcctbx0.substvars debian/libcctbx0/usr/lib/aarch64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_pdb.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcctbx.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libspotfinder.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/librstbx.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_minpack.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_slatec.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_masks.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libasymmetric_map.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libomptbx.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_tls.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_mtz.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_xplor.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libdxtbxspotfinder.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcbf-private.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libccp4io.so.0.0.1 + dpkg-shlibdeps -Tdebian/libcctbx0.substvars debian/libcctbx0/usr/lib/aarch64-linux-gnu/libsmtbx_refinement_constraints.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_pdb.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcctbx.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libspotfinder.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcctbx_sgtbx_asu.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/librstbx.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_masks.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_slatec.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_minpack.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libasymmetric_map.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libomptbx.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libmmtbx_tls.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_mtz.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libiotbx_xplor.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libdxtbxspotfinder.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libcbf-private.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libann_adaptor.so.0.0.1 debian/libcctbx0/usr/lib/aarch64-linux-gnu/libccp4io.so.0.0.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged install -m0755 -d debian/python3-cctbx/DEBIAN - dpkg-shlibdeps -Tdebian/python3-cctbx.substvars debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reduce_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/math/tests/tst debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/error/tst_error debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2 debian/python3-cctbx/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem debian/python3-cctbx/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy debian/python3-cctbx/usr/bin/cctbx_blobs debian/python3-cctbx/usr/bin/cctbx.find_distances debian/python3-cctbx/usr/bin/cctbx.sym_equiv_sites debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry debian/python3-cctbx/usr/bin/cctbx.getting_started debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups debian/python3-cctbx/usr/bin/cbflib.tst_memory + dpkg-shlibdeps -Tdebian/python3-cctbx.substvars debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reduce_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_special_position debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_geometrical_hydrogens debian/python3-cctbx/usr/lib/cctbx/python3.13/smtbx/refinement/constraints/tests/tst_reparametrisation debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/serialization/tst_base_256 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_svd debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_householder debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_cholesky debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/matrix/tests/tst_givens debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/math/tests/tst debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/lbfgs/tst_lbfgs debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/error/tst_error debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_4 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_unsigned_float_arithmetic debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_vec3 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_sym_mat3 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_ref_matrix_facet debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_mat3 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_3 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_rectangular_full_packed debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_optional_copy debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_5 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_2 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_af_1 debian/python3-cctbx/usr/lib/cctbx/python3.13/scitbx/array_family/tst_accessors debian/python3-cctbx/usr/lib/cctbx/python3.13/iotbx/pdb/hybrid_36_fem debian/python3-cctbx/usr/lib/cctbx/python3.13/boost_adaptbx/tests/tst_optional_copy debian/python3-cctbx/usr/bin/cctbx_blobs debian/python3-cctbx/usr/bin/cctbx.find_distances debian/python3-cctbx/usr/bin/cctbx.sym_equiv_sites debian/python3-cctbx/usr/bin/cctbx.lattice_symmetry debian/python3-cctbx/usr/bin/cctbx.sys_abs_equiv_space_groups debian/python3-cctbx/usr/bin/cctbx.getting_started debian/python3-cctbx/usr/bin/cctbx.convert_ccp4_symop_lib debian/python3-cctbx/usr/bin/cbflib.tst_memory dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin -dpkg-shlibdeps: warning: 15 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyImport_ImportModule used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyRange_Type used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_glmtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin -dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/libcctbx0/usr/lib/aarch64-linux-gnu/libscitbx_boost_python.so.0.0.1 found in none of the libraries +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: it's probably a plugin +dpkg-shlibdeps: warning: 28 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_HasAttrString: it's probably a plugin -dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_indexing_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: it's probably a plugin dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 15 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reduce_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: it's probably a plugin +dpkg-shlibdeps: warning: 29 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_wigner_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 28 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: it's probably a plugin +dpkg-shlibdeps: warning: 27 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin +dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin -dpkg-shlibdeps: warning: 25 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: it's probably a plugin -dpkg-shlibdeps: warning: 23 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 18 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_statistics_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyDict_Type: it's probably a plugin -dpkg-shlibdeps: warning: 30 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dtrek_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 32 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBytes_FromStringAndSize: it's probably a plugin -dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin -dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_CallFunction: it's probably a plugin +dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin +dpkg-shlibdeps: warning: 21 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/annlib_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_f_model_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 15 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin -dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_asu_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: it's probably a plugin -dpkg-shlibdeps: warning: 18 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 18 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reduce_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin -dpkg-shlibdeps: warning: 29 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_least_squares_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: it's probably a plugin -dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rotamer_fit_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_icsd_radii_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_shelx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_ClearWeakRefs: it's probably a plugin +dpkg-shlibdeps: warning: 136 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_util_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: it's probably a plugin +dpkg-shlibdeps: warning: 18 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_emma_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin -dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adptbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_GetIter: it's probably a plugin -dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/std_pair_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_maximum_clique_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_constraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 30 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_GetIter: it's probably a plugin -dpkg-shlibdeps: warning: 34 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/determine_unit_cell_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_sgtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin -dpkg-shlibdeps: warning: 27 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_RuntimeError: it's probably a plugin +dpkg-shlibdeps: warning: 23 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_math_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: it's probably a plugin dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin -dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_math_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin -dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgsb_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_viewer_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_set_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_HasAttrString: it's probably a plugin -dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Format: it's probably a plugin -dpkg-shlibdeps: warning: 51 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin -dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin -dpkg-shlibdeps: warning: 28 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 30 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyDict_Type: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_boost_thread_test_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_gl_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyList_Append: it's probably a plugin +dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_distltbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 29 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: it's probably a plugin -dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_RuntimeError: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_CallFunction: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_meta_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: it's probably a plugin +dpkg-shlibdeps: warning: 25 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: it's probably a plugin +dpkg-shlibdeps: warning: 21 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_validation_ramachandran_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_asymmetric_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dssp_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_ccp4_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_integration_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_glu_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin -dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_cubicle_neighbors_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_orientation_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cbflib_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_stl_vector_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Clear: it's probably a plugin +dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_python_streambuf_test_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyRange_Type: it's probably a plugin -dpkg-shlibdeps: warning: 17 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin -dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_hough_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin -dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_StopIteration: it's probably a plugin dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_rational_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_indexing_api_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_minpack_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_uctbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: it's probably a plugin dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bandpass_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lbfgs_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_masking_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_sasaki_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_refinement_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_shared_types_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_graph_structure_comparison_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_crystal_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin -dpkg-shlibdeps: warning: 28 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_bruker_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: it's probably a plugin -dpkg-shlibdeps: warning: 23 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin -dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_rigid_body_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_dsn6_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_random_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_ab_initio_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_chemical_elements_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyList_New: it's probably a plugin +dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_tiny_pse_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_StopIteration: it's probably a plugin +dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_Type: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 30 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_metric_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_translation_search_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBytes_AsString: it's probably a plugin -dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin -dpkg-shlibdeps: warning: 22 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_CallFunction: it's probably a plugin dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_symmetry_constraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin +dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_secondary_structure_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_primitive_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_cartesian_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_CallFunction: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_hydrogens_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 15 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_french_wilson_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_maptbx_bcr_bcr_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: it's probably a plugin -dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: it's probably a plugin -dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_structure_factors_direct_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin +dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/fable_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: it's probably a plugin dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_reference_coordinate_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 21 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_imageset_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: it's probably a plugin -dpkg-shlibdeps: warning: 21 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_symmetry_search_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_graphics_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_iso_surface_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/spotfinder_dxtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_flumpy.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBuffer_IsContiguous: it's probably a plugin -dpkg-shlibdeps: warning: 136 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_xplor_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_detectors_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_xray_observations_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_probe_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_HasAttrString: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_connected_component_algorithm_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_adp_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_Size: it's probably a plugin +dpkg-shlibdeps: warning: 22 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_shared_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PySlice_Type: it's probably a plugin +dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_sparse_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: it's probably a plugin dpkg-shlibdeps: warning: 23 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin -dpkg-shlibdeps: warning: 25 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simulation_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_clustering_algorithm_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_neutron_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_Type: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_pair_interaction_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_wavelengths_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_fonts_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_anharmonic_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyComplex_FromDoubles: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_cif_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_scalepack_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_dmtbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyRange_Type: it's probably a plugin +dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_fp_fdp_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_utility_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_bulk_solvent_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/ccp4io_adaptbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_IsInstance: it's probably a plugin +dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_tuple_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_RuntimeError: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_rsr_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_henke_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_array_family_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_New: it's probably a plugin -dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cma_es_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_masks_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_bpcx_detector_model_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_shared_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 4 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_simage_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_fftpack_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/omptbx_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_optional_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_r3_utils_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_xray_scattering_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_mosaic_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/regression_test_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: it's probably a plugin dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/rstbx_diffraction_fastbragg_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin -dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_python_hybrid_times_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_covalent_radii_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_geometry_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PySlice_Type: it's probably a plugin -dpkg-shlibdeps: warning: 29 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_optimise_amplitudes_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: it's probably a plugin -dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_masks_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_SetString: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/smtbx_stl_map_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 16 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_breadth_first_search_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_CallFunction: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_building_loop_closure_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_array_family_flex_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyIter_Next: it's probably a plugin +dpkg-shlibdeps: warning: 51 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_tls_decompose_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyErr_Occurred: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ramachandran_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: it's probably a plugin dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_mtz_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_GetItem: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_multipolar_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_asa_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_sphere_surface_sampling_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: it's probably a plugin +dpkg-shlibdeps: warning: 9 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_dynamics_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 5 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_merging_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin +dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_den_restraints_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyExc_IndexError: it's probably a plugin dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_lstbx_normal_equations_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_FromDouble: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_eltbx_attenuation_coefficient_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromUnsignedLong: it's probably a plugin +dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/boost_adaptbx_graph_min_cut_max_flow_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin dpkg-shlibdeps: warning: 10 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_pdb_hierarchy_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyObject_GetIter: it's probably a plugin -dpkg-shlibdeps: warning: 32 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_alignment_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_Type: it's probably a plugin +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_covariance_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_max_lik_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin +dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_scaling_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyFloat_Type: it's probably a plugin dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_linalg_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_NoneStruct: it's probably a plugin -dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_geometry_clash_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_Type: it's probably a plugin -dpkg-shlibdeps: warning: 8 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/scitbx_suffixtree_single_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyList_Type: it's probably a plugin -dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/gltbx_quadrics_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol _Py_Dealloc: it's probably a plugin -dpkg-shlibdeps: warning: 20 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/cctbx_miller_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyRange_Type: it's probably a plugin +dpkg-shlibdeps: warning: 25 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_image_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyUnicode_FromStringAndSize: it's probably a plugin +dpkg-shlibdeps: warning: 23 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_model_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 34 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/mmtbx_ncs_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyLong_Type: it's probably a plugin +dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/iotbx_wildcard_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyBool_FromLong: it's probably a plugin +dpkg-shlibdeps: warning: 3 other similar warnings have been skipped (use -v to see them all) +dpkg-shlibdeps: warning: debian/python3-cctbx/usr/lib/python3/dist-packages/dxtbx_format_nexus_ext.cpython-313-aarch64-linux-gnu.so contains an unresolvable reference to symbol PyTuple_Type: it's probably a plugin +dpkg-shlibdeps: warning: 7 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/libcctbx0/DEBIAN install -p -m0644 debian/.debhelper/generated/libcctbx0/triggers debian/libcctbx0/DEBIAN/triggers @@ -51442,53 +51481,53 @@ dh_numpy3: skipping binary package libcctbx-dev which does not depend on the NumPy C ABI mv debian/python3-cctbx.substvars.new debian/python3-cctbx.substvars dh_gencontrol -O--buildsystem=pybuild - install -m0755 -d debian/libcctbx0/DEBIAN - echo misc:Depends= >> debian/libcctbx0.substvars - echo misc:Pre-Depends= >> debian/libcctbx0.substvars - install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN - dpkg-gencontrol -plibcctbx0 -ldebian/changelog -Tdebian/libcctbx0.substvars -cdebian/control -Pdebian/.debhelper/libcctbx0/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libcctbx0-dbgsym -DDepends="libcctbx0 (= \${binary:Version})" -DDescription="debug symbols for libcctbx0" -DBuild-Ids="0cafea64204b90c9b31e433848a992ef80e887bf 0d4d4a2d3e8d8aadfaf0c85e97a8cdd8b1d6cf18 0da01bc76df178a4c91c90245c484d95ef2dfcc1 118ec818e2a8aef469e456320fff8e209a5c6203 11d2050414411f11f3ac0cec16150e3ca78e3147 14dde896fddfd8d0dc7216b265113be76a47cf3f 160eee3a0a79ac061fdc3a16ead64b169795f1c2 25a475e4ac49f117c5cce9db51f3977d4c13dc46 35b8d88d46ce42e23b0e342eb1b5385ae44be197 4184449d13b44fd3e2a5697e24e6277267794cf1 44c050ca42aedecee4c12dc3e9a3ff17790bae32 6f2e55bdc4eb3f7c4906b53a113ccb49023e8e9d 78e3a204d1b5cfef7a843937eea3328f66ca6cef 976f9af382034d74bd0ee2f7e1de13cc6f67ff6e 9a5e3044aa965861d92ecb6134de5a9b24895f25 cc25063d831d6cfb11fc27d15fdbe86e8184983b eb58622dc1e64d09adabfb5df2c69d5a5139f084 fd9dcac506af1011b4fded922a28cd02d5e62ab9 fdaf7cfeb3a53844ab34ab00b9de58ed723a96da" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/python3-cctbx/DEBIAN echo misc:Depends= >> debian/python3-cctbx.substvars echo misc:Pre-Depends= >> debian/python3-cctbx.substvars install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-cctbx -ldebian/changelog -Tdebian/python3-cctbx.substvars -cdebian/control -Pdebian/.debhelper/python3-cctbx/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-cctbx-dbgsym -DDepends="python3-cctbx (= \${binary:Version})" -DDescription="debug symbols for python3-cctbx" -DBuild-Ids="00f6db8b143b8ba346bb1077a68cde00dbf970f5 02952fcbd0d8e0cb50fb0adefd729709ff0b7bc2 0413f9464e952f3a7f34c323346769d62608b7be 04ec33ab729bc078144b77840a820e48c822d33a 05e05a3b5c4801822e037923c3bab5d8db64e7c7 08052f75429e756243d4396aba0dd359d7dd0246 099e830caebcfd078bea058ab2f210e055b84572 0ad154b81cda01c07bb53ee871353d1ff94018a6 0d11e0bf888a20ceb963f9b0dd1a42a1ce841ba4 0d857a44edf46fb7c126509a234ffe37c623a7f1 0f58bd4bbfd4fad7e66edefe3d77b9f9e286d27c 102b63799a2a5f2810070ba75b9abf64bf1336f6 1049269b8cdfef48c93cc10c3b8dbeeb3f78b21c 122114e4e733ec33f4752e619c8194a4d1ea6684 13588e16dfef3263de4d5f861fd39eb760be1299 157b502b74b8c59561fb11e696fe4d39467b73c7 16024ca0c77ae2cbc971376801f2d3488ba9ea41 1717a6767994a96d771baa7ec376b728f001e9f4 1b1dbfe5f5f2b884e016bd882534ad854e0936de 1b50f08ee77934ab66984f41f12225311e21620f 1c079dec16b18813b411b32af0936fe5cb0d6c28 1e7b856f5cc756f84b2fc2e6d951ea745f41dbd5 1fc94d1a1ea10bfa27403a6955f184f8715ced72 21d0553ec58944508559970bf8d27c9c5c49ed3b 22bb91a91be241821f3f5147a53c039505acd59c 260cffb6907d0a8531ba8d8bcadfe0af9ddc4391 26896b49c836b0231489efd0e19a1e06814e627d 26e926a52700ab297cfd032870c524d58125c999 2726a3b78782e8f5f82d1c4544b2a7a6c45bb4ed 2904d6912f857c1e4400e4929a0e91e4378ed21c 29d0d4d37a45886fd9e2473f0e9e45dc85148f1b 2a21b76ba6651276c81ce73e42002b271ee094a2 2bc001bca30b7fa380262a92924087fa3b01a842 2d482727fb4c67f1f0f71bce0508a66dda3ed0dd 2d56408c49acce28a182ab511565c89da1232210 2f4b9969d52663feb89a01081a5707bc9d7feba9 3040e48480126af60bb155d07810e02172dcb645 31b1c2b7faa071293c701216d0b7b85a75da27d0 32aa6fd72b7b21f5674f4ff8b84faade08a25866 357caefaedf181e2022b4c74cad0810708560530 35c498d7abcdfce3dbdd5a5e437028961ab6c628 36a870c133e0ed3929afe631b989d53b97f09565 36fbb9939943923ecf118bf8865e02fe8a6e98e7 3778b649c3dd2b7b491fcffc3391f9efb77cff54 3a046bb31784f76441a4a69db76dcd3aba40047f 3abf498075d978c4626ff1a71ade145500f37f0e 3b570e367f1d60a9fbf3c6e03f76091b80005ef7 3c45996be5bcbd794dd603757efdc79a3c63a759 3ca034ed73cbccffda9b3bd607679f51eec07c91 3d4b57eab947dff32acbea295100f878ef05a625 4027d192ee3cd5c97d2e0ac4f112d7541e7de020 40c69357e1922e409df5931cad1ec115350b3a90 456825da69c1ef24c308b61601ced5007a86b492 463fd86805fb63d91e644579d0e5f9e8e787880f 4800ddb438db4c03ac9306284ec78466b0916b5a 484b541d0c9edd1dd9d0c69afded9aa879abd3fa 4881b0ed5ac4338e62a79987db6a220a32d1732e 493f23adfcd0c41e7751b3991bf572d103ec0a86 4a7241b8c80b07cada8b1c7b224433f57851e88c 4c6da5769b86d05be870c0c99e008b268129b048 4dbeb1a9ae934b1fd71b5ead8c205f043c63d9af 4e7f7cebc52bbc273339082de6623c24afe89a15 518ed2db41b81199a4cdb31dc986b668130583d1 5447f14ad246273dde85fcfe7c873910e3983133 54e4e2d02ca30cf20bcc6febada82a5330bb03d7 5577b228b9ef2ed6c9bf7c854e8b071aa2d22cc2 56487cc5c73b2a7310add6d465aef3e8e874ddd0 5653a1e6ee19f15602cbb99f35a77970b10a13f7 5669d605d1539104416627aa0f0dd3fa35279300 573a1f5636fb89a795896e0afb293a3a62b03a92 57826d17f0e1c6f0a71087b6b8f4b587a8a3fb62 57ae128afb5c5d54a0450ba7fd2e0ed55b9c6741 58322cabb30799a9ea61e6169bf30c097784f520 584b3be363cfc0c735d008a8c04a582856155348 5855a6801bd8a5faacf4b8826da062846cf3be2b 5a9986c210d19abfbbcc5ce9c7ee679dc7fde4db 5d448d58ce97a1eaf869362b11a329ae86ee9fa1 5d93108c52cba29ba31db84c41df656e5125f3f0 60bcf999266cdea627212e502073a3ae5e3f0b4f 61d65108d3e853a9ac43de71e46b41dc0d4f4e80 6518b06ab4a1caaa4f57e3e57bd84171ca598acd 658067b253ad65646bd0f4aeb63dfc3a35f9ca41 65c299264a019f7ea6b8cbd27d879db79350b6ee 66c6b6413ba157bfa5cab4cbea9fffa26e2d481f 67c7b1a3fb9ac8a55299dd85f46c6e9e195900ec 67e09bd535c460735aa5a52663e4e88faf8a1ee0 6818af3bcc9ec1140533a1816194d41e82eb6bc6 692f6177f061d498a0238b7a688f51a73c75dd34 6b7a820f4997d53aa1abfe97f4aaae0315833c42 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8bd6bf0ddad1cf9ab4ba5e356e8ce312daf15b12 8c2f3d3a728b142aaafd39ffa67f1d96403d0bdb 8d376b9c7b16cc70947132fab75dd95cbe15bf4f 8d4addc8a0bc6f127d80a445d37a47e86781bffe 8fcf05ef09986b8686ae745447715422c5105f71 8fd8f9bcd3b82c90ea19e02b23347164d3d26a9d 9007262c541b204f48af437c4d26a61511330f21 9046abe154ca73054c61a41ffd64171a5ef7ab41 91af4222d3f6787bf715bf5aad9f650db05f838a 91e9267355a0c000b1562cb16c3d39d8acff609f 968406c5778b557f4e60fa19ce00867fbff3f743 9884fdfd29dafd6360037645a8134bf518666f7c 994f8fe2afbef9e8d1206e76309efd3986e745c0 99e85d95dfbc0952bb8f3744a91db78808415039 9aa5a0ad41ae20dd89a62af11d92177a643d64dd 9b180e3fb315750bd914cdaf26072723ceb8e0bf 9d161c1109d1021ff37c041385364d74f7003c2d 9ec3a753a4ffbf996fd22f7b15eda2e7d2f3f7ea 9f45773c8aa16a9895bf091c2812a68d1e052533 a004962c47d66facd14714a4c3e7e3d481317b46 a09d2a4facf3c50ddff9e34aa8b67c535f985db5 a2fab53812526902a3693b86e01aeb53d2f58daa a36f5c3b3ec70949e818c86c953bbbc993c16534 a3b431d12b84d3ecb463b812c21881c5e389b47a a3ee8d12395901abe7aea3222fb5e7605bc17ef0 a489ad3b484b0ddb2f93c870163a403c8157dd2e a5310545b4fa9225f43f79c477988c23d0572eb6 a8fd90b450c218747834ae7ff94715dd4c8fa022 aba5c6798c2557ef7d5daf5d477971a7d55472ad aca71d8f69b7729f7db1180d5b940fb51299e387 ad84b06d6381e4f0156bf4b757e511b57de67dca afa82d042cc413ea2da247744a3a942e0ef66409 b04ad8603fde263c51f52d83d51d997d2670aa9f b1b70b45662c2a68ca46ef3494df279fcaa8d359 b22b69c3b2393a1396a865dff7c58264b67070cf b4d1a3114f6c0c4c73da4ffc7662ee338b13fa72 b4e6e5a57c737f6e2261d798c31834bbd70f3fd8 b587b7e84b522f48970ac7eb288750a9c145d8de b6b161536d93758182ac265c3386f551df3490f6 b750b809b36392cce497325c2c1c139e313a4668 b7d86924211d9a54fc8618739996ed36751401d9 b824741dc64342b81d181877ece4b59a1f06f8c6 b846a3dbc66d8e2d149acd67401a147c7639c0dc b89275b069d651fc2ad3a6d717020d386548c64a b896ac757f3ceeae6d0e622768fd1b9bbc63f96f b98b9797c5e9f820823857661546d816bbf63803 ba586bd0b9f6b0923d9ad7408144e000e2fad8e8 bb81325f81eb64b676918112c6f73a2c2e4563c2 bcbb7e97773467ef7a7751009fc7ad0996a423ef bd0414b4cb0ecf7cc9def6fd895ca482868298e1 bd137e107859d1699926647365f3068aaa26f77a c29daabe3ca3d6a06bf2083d0de0d502d965d82b c378611e9f1550e14047353d6c0f4c6b90362cec c8f5a48607c31b7b1695c9bda30950304a81096c c9cf8c46ae1f94e4f1dcb08b732d1eb0efff3630 caa5d6640b2cf2b535d3c8869ac4c0cdac353c4f caf3d7ab72cbaf5cb3f5affc3a0c3a27d5754a8a cf08283ff3853538101043106a21f81906338575 d053f36d0d32e4c9c35421aae176cae2306d0e80 d2e9a282e8d50b3e35ed9e62ae00c9d84f8ff0e5 d431e5aa599fe712e4775680bf5d099c9efab69d d45b06ed4f9a539b204c7873781fa3e3d11b5160 d50b8ff3b884cf273d6a336265e12a4b3a1e42a9 d5196250486a5921b6f55a179588e4e02111ccb4 d5ce1143bc28076d81f434d59368d3b3f9a40c1a d6ef8afc0994d19ae46fc9e9af0b7fe39307f7a6 dba22288bd091fa3336a66dc873e8a8fd732239f dbbcfc2569564149a7e8c1973f3d0eb5ad3270da dd9b85221b3ca440c152ea275fab70522094b396 df0b653796eb93bf3dbcc51c5cc4c3ae2c21f474 e158152cb8321cec437fb01167c8f6e8ac8df525 e68cc90577542fbbfc1c84146b5d4d652c8b4ff2 e73d0bbf08b5dbd1bcf22e727b2cad89a4fe27db e74aa7cb0ddab8bc7b0e712bbcc4f1404df653bd eda712ae1bc61aa6b5bbe76cca7c463970c2181c ef57db0f3c8887e228a9f903abf3a7cb5b19a2e7 ef9cc0bc8c9493fcb6eed2e7071b07f65693a139 f05dcc72000ae497b5bb00e66f981ddf07326637 f1b8c0766fdf878b21dbd2d7469c700332680282 f48fd577c6db45cec3beeb1e577c3f04b49bc85f f5cee32038753779efafba021a0173d1d4733b50 f5e03faf3cc16ed90dcfc5fa1062fe70a7b9e460 f92b42b58c0e780a5fadf7593ccf522851ef6821 f93febbac6369db30af31342ef752131d1b06734 f9c7d3fbdf0a66e0da75e51543e94ba9849b6040 fb37e86be7a3fc967cbb96979edc2caae21328e9 fc6ef957ebaf2a92d1c30ded846398b769e9da50 fcd01cd890c75e7f8a08433470836ecd4e61d515 feb9a9cca1bacc6551ae837d9115fbf1bfbf4f7a" -DSection=debug -UMulti-Arch -UReplaces -UBreaks + install -m0755 -d debian/libcctbx0/DEBIAN + echo misc:Depends= >> debian/libcctbx0.substvars + echo misc:Pre-Depends= >> debian/libcctbx0.substvars + install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN + dpkg-gencontrol -plibcctbx0 -ldebian/changelog -Tdebian/libcctbx0.substvars -cdebian/control -Pdebian/.debhelper/libcctbx0/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libcctbx0-dbgsym -DDepends="libcctbx0 (= \${binary:Version})" -DDescription="debug symbols for libcctbx0" -DBuild-Ids="0cafea64204b90c9b31e433848a992ef80e887bf 0d4d4a2d3e8d8aadfaf0c85e97a8cdd8b1d6cf18 0da01bc76df178a4c91c90245c484d95ef2dfcc1 118ec818e2a8aef469e456320fff8e209a5c6203 11d2050414411f11f3ac0cec16150e3ca78e3147 14dde896fddfd8d0dc7216b265113be76a47cf3f 160eee3a0a79ac061fdc3a16ead64b169795f1c2 25a475e4ac49f117c5cce9db51f3977d4c13dc46 35b8d88d46ce42e23b0e342eb1b5385ae44be197 4184449d13b44fd3e2a5697e24e6277267794cf1 44c050ca42aedecee4c12dc3e9a3ff17790bae32 6f2e55bdc4eb3f7c4906b53a113ccb49023e8e9d 78e3a204d1b5cfef7a843937eea3328f66ca6cef 976f9af382034d74bd0ee2f7e1de13cc6f67ff6e 9a5e3044aa965861d92ecb6134de5a9b24895f25 cc25063d831d6cfb11fc27d15fdbe86e8184983b eb58622dc1e64d09adabfb5df2c69d5a5139f084 fd9dcac506af1011b4fded922a28cd02d5e62ab9 fdaf7cfeb3a53844ab34ab00b9de58ed723a96da" -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/libcctbx-dev/DEBIAN echo misc:Depends= >> debian/libcctbx-dev.substvars echo misc:Pre-Depends= >> debian/libcctbx-dev.substvars dpkg-gencontrol -plibcctbx-dev -ldebian/changelog -Tdebian/libcctbx-dev.substvars -cdebian/control -Pdebian/libcctbx-dev - chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN/control - dpkg-gencontrol -plibcctbx0 -ldebian/changelog -Tdebian/libcctbx0.substvars -cdebian/control -Pdebian/libcctbx0 chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-cctbx -ldebian/changelog -Tdebian/python3-cctbx.substvars -cdebian/control -Pdebian/python3-cctbx + chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN/control + dpkg-gencontrol -plibcctbx0 -ldebian/changelog -Tdebian/libcctbx0.substvars -cdebian/control -Pdebian/libcctbx0 chmod 0644 -- debian/libcctbx-dev/DEBIAN/control chmod 0644 -- debian/libcctbx0/DEBIAN/control chmod 0644 -- debian/python3-cctbx/DEBIAN/control dh_md5sums -O--buildsystem=pybuild - install -m0755 -d debian/libcctbx0/DEBIAN install -m0755 -d debian/libcctbx-dev/DEBIAN install -m0755 -d debian/python3-cctbx/DEBIAN + install -m0755 -d debian/libcctbx0/DEBIAN cd debian/libcctbx0 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libcctbx-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/python3-cctbx >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libcctbx0/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN + chmod 0644 -- debian/libcctbx-dev/DEBIAN/md5sums cd debian/.debhelper/libcctbx0/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libcctbx0/dbgsym-root/DEBIAN/md5sums - chmod 0644 -- debian/libcctbx-dev/DEBIAN/md5sums chmod 0644 -- debian/python3-cctbx/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-cctbx/dbgsym-root/DEBIAN cd debian/.debhelper/python3-cctbx/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-cctbx/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/libcctbx0 .. - dpkg-deb --root-owner-group --build debian/libcctbx-dev .. - dpkg-deb --root-owner-group --build debian/python3-cctbx .. dpkg-deb --root-owner-group --build debian/.debhelper/libcctbx0/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/libcctbx-dev .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-cctbx/dbgsym-root .. + dpkg-deb --root-owner-group --build debian/python3-cctbx .. +dpkg-deb: building package 'libcctbx0-dbgsym' in '../libcctbx0-dbgsym_2025.2+ds2+~3.23.0+ds1-1_arm64.deb'. +dpkg-deb: building package 'libcctbx-dev' in '../libcctbx-dev_2025.2+ds2+~3.23.0+ds1-1_arm64.deb'. dpkg-deb: building package 'python3-cctbx-dbgsym' in '../python3-cctbx-dbgsym_2025.2+ds2+~3.23.0+ds1-1_arm64.deb'. dpkg-deb: building package 'libcctbx0' in '../libcctbx0_2025.2+ds2+~3.23.0+ds1-1_arm64.deb'. -dpkg-deb: building package 'libcctbx-dev' in '../libcctbx-dev_2025.2+ds2+~3.23.0+ds1-1_arm64.deb'. -dpkg-deb: building package 'libcctbx0-dbgsym' in '../libcctbx0-dbgsym_2025.2+ds2+~3.23.0+ds1-1_arm64.deb'. dpkg-deb: building package 'python3-cctbx' in '../python3-cctbx_2025.2+ds2+~3.23.0+ds1-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../cctbx_2025.2+ds2+~3.23.0+ds1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../cctbx_2025.2+ds2+~3.23.0+ds1-1_arm64.changes @@ -51497,12 +51536,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2671576/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2671576/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/1804204 and its subdirectories -I: Current time: Fri Oct 24 15:01:00 -12 2025 -I: pbuilder-time-stamp: 1761361260 +I: removing directory /srv/workspace/pbuilder/2671576 and its subdirectories +I: Current time: Fri Nov 27 23:40:39 +14 2026 +I: pbuilder-time-stamp: 1795772439